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TD 225 
. C43 
A482 
2010 
Copy 1 


s 

Region III 

Region III 

EPA 903-R-10-00 

L-,,.,.wi„,,w..;al Protection 

Chesapeake Bay 

Water Protection 

CBP/TRS 301-10 

Agency 

Program Office 

Division 

May 2010 


In coordination with the Office of Water/Office of Science and Technology, Washington, D C., and the states of Delaware, 
Maryland, New York, Pennsylvania, Virginia and West Virginia and the District of Columbia 


SLiBRAl 


Oh CONGRESS 


^ 




Ambient Water Quality Criteria 
for Dissolved Oxygen, Water 
Clarity and Chlorophyll a for the 
Chesapeake Bay and Its Tidal 
Tributaries: 2010 Technical 
Support for Criteria Assessment 
Protocols Addendum 

May 2010 


I 


Ambient Water Quality Criteria for Dissolved 
Oxygen, Water Clarity and Chlorophyll a for the 
Chesapeake Bay and Its Tidal Tributaries: 2010 
Technical Support for Criteria Assessment 

Protocols Addendum 

May 2010 

U.S. Environmental Protection Agency 
Region III 

Chesapeake Bay Program Office 
Annapolis, Maryland 

and 

Region III 

Water Protection Division 
Philadelphia, Pennsylvania 

in coordination with 

Office of Water 

Office of Science and Technology 
Washington, D.C. 

and 

The states of 

Delaware, Maryland, New York 
Pennsylvania, Virginia and 
West Virginia and the District of Columbia 


Library of Congress 



2012 


545093 
































Contents 


Acknowledgements. 3 

I. Introduction.5 

Literature cited.6 


II. Designated Use Boundaries: Episodic Pycnocline Application and 

Expanded Designated Uses.8 

Background.8 

Revising a Procedural Anomaly in the Designated Use Delineation.9 

Identification of a Procedural Anomaly.9 

Episodic Pycnocline Criteria Assessment Protocol Modification.10 

Expanded Application of Deep-Water and Deep-Channel Designated Uses.11 

Review of Designated Use Definitions.11 

Mesohaline Segments Expanded Designated Uses.12 

Literature Cited. 14 

III. Biologically-based Reference Curve: Revisions to the Methodology and 

Applications.15 

Background.15 

Issues with Dissolved Oxygen Criteria Assessment with the Available Previously 

Published Biologically-based Reference Curves.16 

Updates to Dissolved Oxygen Biologically-based reference Curve Derivation 

Methodology.17 

Restrict dataset to data collected beginning in 1996. 18 

Use sequential 3-year time periods rather than single years.18 

Screening criteria sample size n>10.19 

Screening criteria standard deviation < 1.0.19 

Definition of healthy benthic macroinvertebrate reference community 

conditions.20 

Use Grand Score in computations involving fixed station data.20 

Summary of Recommendations.21 

Application of a Reference Curve for Open-Water 30-day Mean Dissolved Oxygen 

Criteria: Summer Season.23 

Application of a Reference Curve for Deep-Water Mean Dissolved Oxygen 

Criteria.23 

Application of a Reference Curve for Deep-Channel Instantaneous Minimum 

Dissolved Oxygen Criterion.24 

Comparisons of Degraded Reference Benthic Communities with the Published 

Deep Channel Reference Curve .25 

Rationale for Acceptable Exceedances of the Deep Channel Instantaneous 

Minimum Dissolved Oxygen Criterion.26 

Assessment of Summer Season Dissolved Oxygen Criteria.27 


1 

































Literature Cited 


28 


IV. Revisions to the Chlorophyll a Criteria Assessment Methodology.31 

Background.31 

Review of the Current Chlorophyll a Criteria Attainment Assessment Procedure: 

Method and Assumptions.32 

Chlorophyll a: Data Skewness, Log Transformation and the Seasonal Mean 

Calculation.34 

Log normal character of chlorophyll a data.34 

James River focused analyses of log transformed chlorophyll a data for 

normality.35 

Chlorophyll a criteria Assessment Protocol Refinements using Log- 

Transformations.36 

Implications of the Revised Assessment Protocol.37 

Literature Cited.38 


Acronyms.41 

Appendices 

A. IBI Sample Size and Standard Deviations on 1BI Scoring When Screening 

Segments for Reference Community characterization.42 

B. Shape of the Biologically-based Reference Curve.46 

C. Derivation of the Deep-Water Biologically-Based Reference Curve.49 

D. History of EPA Guidance Regarding the Deep-Channel Reference Curve.52 

E. James River Chlorophyll a Data Normality Analysis Checking Normality of Log- 

Transformed Chlorophyll a Data.54 

F. SAS Computer Code for James River VA Chlorophyll a Normality Tests, Spring and 

Summer Season.57 


i 



















Acknowledgements 


This fifth addendum to the EPA April 2003 publication of Ambient Water Quality Criteria for 
Dissolved Oxygen, Water Clarity and Chlorophyll a for the Chesapeake Day and Its Tidal 
Tributaries (Regional Criteria Guidance) was developed and documented through the 
collaborative efforts of members of the Chesapeake Bay Program's (CBP) Criteria Assessment 
Protocols Workgroup and the Water Quality Goal Implementation Team. 

PRINCIPAL AND CONTRIBUTING AUTHORS 

The following are principal and contributing authors of this addendum: Peter Tango, U.S. 
Geological Survey/Chesapeake Bay Program Office; Jeni Keisman, University of Maryland 
Center for Environmental Science/Chesapeake Bay Program Office; Richard Batiuk, U.S. EPA 
Region 3 Chesapeake Bay Program Office; Elgin Perry, Statistical Consultant, and Jackie 
Johnson, Interstate Commission on the Potomac River Basin/Chesapeake Bay Program Office. 

CRITERIA ASSESSMENT PROTOCOL WORKGROUP 

Peter Tango, Chair, U.S. Geological Survey/Chesapeake Bay Program Office; Chery l Atkinson, 
U.S. EPA Region 3, Water Protection Division; Harry Augustine, Virginia Department of 
Environmental Quality; Mark Barath, U.S. EPA Region 3, Water Protection Division; Tom 
Barron, Pennsylvania Department of Environmental Protection; Stephen Cioccia, Virginia 
Department of Environmental Quality; Richard Eskin, Maryland Department of the 
Environment; Sherm Garrison, Maryland Department of Natural Resources; Darryl Glover, 
Virginia Department of Environmental Quality; Rick Hoffman, Virginia Department of 
Environmental Quality; Jackie Johnson, Interstate Commission on the Potomac River 
Basin/Chesapeake Bay Program Office; Jeni Keisman, University of Maryland Center for 
Environmental Science/Chesapeake Bay Program Office; Susan McDowell, United States 
Environmental Protection Agency Region III; Larry Merrill, United States Environmental 
Protection Agency; Bruce Michael, Maryland Department of Natural Resources; Ken Moore, 
Virginia Institute of Marine Science; Shah Nawaz, District Department of the Environment; 
Jennifer Palmore, Virginia Department of Environmental Quality; Tom Parham, Maryland 
Department of Natural Resources; Elgin Perry, Statistics Consultant; Charlie Poukish, Maryland 
Department of the Environment; Tish Robertson, Virginia Department of Environmental 
Quality; Matt Rowe, Maryland Department of the Environment; John Schneider, Delaware 
Department of Natural Resources and Environmental Control; Gary Shenk, United States 
Environmental Protection Agency; Donald Smith, Virginia Department of Environmental 
Quality; Scott Stoner, New York State Department of Environmental Conservation; Matt Stover, 
Maryland Department of the Environment; Bryant Thomas, Virginia Department of 
Environmental Quality; Mark Trice, Maryland Department of Natural Resources; David 
Wolanski, Delaware Department of Natural Resources and Environmental Control. 

WATER QUALITY GOAL IMPLEMENTATION TEAM 

Dave Hansen, Co-Chair, University of Delaware; Robert Koroncai, Co-Chair, U.S. 
Environmental Protection Agency Region 3 Water Protection Division; Katherine Antos, 
Coordinator, Chesapeake Bay Program Office, U.S. Environmental Protection Agency; Victoria 


3 


Kilbert, Staff, Chesapeake Research Consortium; Rachel Streusand, Staff, Chesapeake Research 
Consortium; Rich Batiuk, U.S. Environmental Protection Agency Region 3 Chesapeake Bay 
Program Office; Steve Bieber, Metropolitan Washington Council of Governments; Patricia 
Buckley, Pennsylvania Department of Environmental Protection; Collin Burrell, District 
Department of the Environment; Monir Chowdhury, District Department of the Environment; 
Frank Coale, University of Maryland; Lee Currey, Maryland Department of the Environment; 
James Davis-Martin, Virginia Department of Conservation and Recreation; Chris Day, U.S. 
Environmental Protection Agency Region 3; Ron Entringer, New York Department of 
Environmental Conservation; Richard Eskin, Maryland Department of the Environment; 
Normand Goulet, Northern Virginia Regional Commission; Krista Grigg U.S. Navy; Mike Haire, 
U.S. Environmental Protection Agency Office of Water; Jeffrey Halka, Maryland Geological 
Survey; Carlton Haywood, Interstate Commission on the Potomac River Basin; Dave Heicher, 
Susquehanna River Basin Commission; Rick Hill, Virginia Department of Conservation and 
Recreation; Beth Horsey, Maryland Department of Agriculture: Ruth Izraeii, U.S. Environmental 
Protection Agency Region 2; Bill Keeling, Virginia Department of Conservation and Recreation; 
John Kennedy, Virginia Department of Environmental Quality; Teresa Koon, West Virginia 
Department of Environmental Protection; Felix Locicero, U.S. Environmental Protection Agency 
Region 2; Charles Martin, Virginia Department of Environmental Quality; Bruce Michael, 
Maryland Department of Natural Resources; Matt Monroe, West Virginia Department of 
Agriculture; Dave Montali, West Virginia Department of Environmental Protection; russel 
Morgan, U.S. Department of Agriculture Natural Resource Conservation Service; Matt Mullin, 
Chesapeake Bay Commission; Kenn Pattison, Pennsylvania Department of Environmental 
Protection; Russ Perkinson, Virginia Department of Conservation and Recreation; Alan Pollock, 
Virginia Department of Environmental Quality; Marel Raub, Chesapeake bay Commision; John 
Rhoderick, Maryland Department of Agriculture; John Schneider, Delaware Department of 
Natural Resources and Environmental Control; Mohsin Siddique, D.C. Water and Sewer 
Authority; Jennifer Sincock, U.S. Environmental Protection Agency Region 3; Randolph Sovic, 
West Virginia Department of Environmental Protection; Tanya Spano, Metropolitan Washington 
Council of Governments; Ann Swanson, Chesapeake Bay Commission; Jennifer Volk, Delaware 
Department of Natural Resources and Environmental Control; Robert Yowell, Pennsylvania 
Department of Environmental Protection. 


4 


CHAPTER 1 


Introduction 

In April 2003, the U.S. Environmental Protection Agency (EPA) published the Ambient Water 
Quality Criteria for Dissolved Oxygen, Water Clarity and Chlorophyll a for the Chesapeake Bay 
and Its Tidal Tributaries which was the foundation document defining Chesapeake Bay water 
quality criteria and recommended implementation procedures for monitoring and assessment 
(U.S. EPA 2003a). In October 2003, EPA published the Technical Support Document for 
Identification of Chesapeake Bay Designated Uses and Attainability which defined the five tidal 
water designated uses to be protected through the published Bay water quality criteria (U.S. EPA 
2003b): 


• Migratory fish spawning and nursery habitat; 

• Open-water fish and shellfish habitat; 

• Deep-water seasonal fish and shellfish habitat; 

• Deep-channel seasonal refuge habitat; and 

• Shallow-water bay grass habitat. 

A total of six addendum documents have been published by EPA since April 2003. Three 
addenda were published documenting detailed refinements to the criteria attainment and 
assessment procedures (U.S. EPA 2004a, 2007a, 2008) previously published in the original April 

2003 Chesapeake Bay water quality criteria document (U.S. EPA 2003a). One addendum 
published Chesapeake Bay numerical chlorophyll a criteria (U.S. EPA 2007b). Another 
addendum addressed detailed issues involving further delineation of tidal water designated uses 
(U.S. EPA 2004b) building from the original October 2003 tidal water designated uses document 
(U.S. EPA 2003b). Finally, one addendum addressed refinements to the Chesapeake Bay 
Program analytical segmentation schemes (U.S. EPA 2005) building from the original U.S. EPA 

2004 document (U.S. EPA 2004c). 

The detailed procedures for assessing attainment of the Chesapeake Bay water quality criteria 
continued to be advanced through the collective EPA, States and District of Columbia 
partnership efforts. These partners continue to develop and apply procedures that incorporate the 
most advanced state-of-the-science, magnitude, frequency, duration, space and time 
considerations with, as available, biologically-based reference conditions and cumulative 
frequency distributions. As a rule, the best test of any new method or procedure is putting it to 
application with partner involvement and stakeholder input. Through the work of its Criteria 
Assessment Protocols Workgroup, the Chesapeake Bay Program partnership has an established 
forum for resolving issues, factoring in new scientific findings, and ensuring implementation of 
consistent bay-wide criteria assessment procedure development and implementation. The 
Workgroup draws upon the talents and input from state, federal, river basin commission and 
academic partners as well as local government and municipal stakeholders. This EPA 2010 
Chesapeake Bay Criteria addendum provides previously undocumented features of the present 
procedures as well as refinements and clarifications to the previously published Chesapeake Bay 
water quality criteria assessment procedures. 


5 



Chapter 2 documents refinements to the procedures for defining Chesapeake Bay designated uses 
and expands the application of the deep-water seasonal fish and shellfish designated use to two 
Chesapeake Bay segments in Maryland's tidal waters. 

Chapter 3 documents refinements and additions to the previously published procedures for 
deriving biologically-based reference curves and recommendations for their application for 
Chesapeake Bay dissolved oxygen criteria assessments. 

Chapter 4 documents refinements and provides recommendations for the procedures assessing 
the previously published numerical Chesapeake Bay chlorophyll a criteria. 

Appendices to these three chapters provide more detailed documentation on derivation of the 
recommended refined criteria assessment procedures. 

This document represents the fifth formal addendum to the original 2003 Chesapeake Bay water 
quality criteria document. As such readers should regard the sections in this document as new or 
replacement chapters and appendices to the original published Bay Criteria report (U.S. 2003a). 
The criteria assessment procedures published in this addendum also replace and otherwise 
supersede similar criteria assessment procedures published in the 2004, 2007 and 2008 addenda 
(U.S. EPA 2003a, 2004a, 2007a, 2007b, 2008). Publication of future addenda by EPA on behalf 
of the Chesapeake Bay Program watershed jurisdictional partners is likely as continued scientific 
research and management applications reveal new insights and knowledge that should be 
incorporated into revisions of state water quality standards regulations in upcoming triennial 
reviews. 


LITERATURE CITED 

U.S. Environmental Protection Agency. 2003a. Ambient Water Quality Criteria for Dissolved 
Oxygen , Water Clarity and Chlorophyll a for the Chesapeake Bay and Its Tidal Tributaries 
(Regional Criteria Guidance). April 2003. EPA 903-R-03-002. Region III Chesapeake Bay 
Program Office, Annapolis, MD. 

U.S. Environmental Protection Agency. 2003b. Technical Support Document for Identification of 
Chesapeake Bay Designated Uses and Attainability. October 2003. EPA 903-R-03-004. Region 
III Chesapeake Bay Program Office, Annapolis, MD. 

U.S. Environmental Protection Agency. 2004a. Ambient Water Quality Criteria for Dissolved 
Oxygen, Water Clarity and Chlorophyll a for the Chesapeake Bay and Its Tidal Tributaries - 
2004 Addendum. October 2004. EPA 903-R-04-005. Region III Chesapeake Bay Program 
Office, Annapolis, MD. 

U.S. Environmental Protection Agency. 2004b. Technical Support Document for Identification of 
Chesapeake Bay Designated Uses and Attainability - 2004 Addendum. October 2004. EPA 903- 
R-04-006. Region III Chesapeake Bay Program Office, Annapolis, MD. 


6 



U.S. Environmental Protection Agency. 2004c. Chesapeake Bay Program Analytical 

Segmentation Scheme: Revisions, Decisions and Rationales 1983-2003. October 2004. EPA 903- 
R-04-008. Region 111 Chesapeake Bay Program Office, Annapolis, MD. 

U.S. Environmental Protection Agency. 2005. Chesapeake Bay Program Analytical 

Segmentation Scheme: Revisions, Decisions and Rationales 1983-2003. 2005 Addendum. 
December 2005. EPA 903-R-05-004. Region III Chesapeake Bay Program Office, Annapolis, 
MD. 

U.S. Environmental Protection Agency. 2007a. Ambient Water Quality Criteria for Dissolved 
Oxygen, Water Clarity and Chlorophyll a for the Chesapeake Bay and Its Tidal Tributaries - 
2007 Addendum. July 2007. EPA 903-R-07-003. Region III Chesapeake Bay Program Office, 
Annapolis, MD. 

U.S. Environmental Protection Agency. 2007b. Ambient Water Quality Criteria for Dissolved 
Oxygen, Water Clarity and Chlorophyll a for the Chesapeake Bay and Its Tidal Tributaries - 
Chlorophyll a Addendum. October 2007. EPA 903-R-07-005. Region III Chesapeake Bay 
Program Office, Annapolis, MD. 

U.S. Environmental Protection Agency. 2008. Ambient Water Quality Criteria for Dissolved 
Oxygen, Water Clarity and Chlorophyll a for the Chesapeake Bay and Its Tidal 
Tributaries—2008 Technical Support for Criteria Assessment Protocols Addendum. September 
2008. EPA 903-R-08-001. Region III Chesapeake Bay Program Office, Annapolis, MD. 


7 




CHAPTER 2 


Designated Use Boundaries: Episodic Pycnocline 
Application and Expanded Designated Uses 

BACKGROUND 

In the 2003 Ambient Water Quality Criteria for Dissolved Oxygen, Water Clarity and 
Chlorophyll a for Chesapeake Day and Its Tidal Tributaries, EPA defined five tidal water 
habitats as designated uses providing the context for setting protective Chesapeake Bay water 
quality criteria (U.S. EPA 2003). Detailed dissolved oxygen criteria were established for 
Chesapeake Bay and its tidal tributaries and embayments tailored to each designated use 
accounting for its variations in space and time. EPA has published and Delaware, Maryland. 
Virginia and the District of Columbia have adopted into their state's water quality standards 
regulations dissolved oxygen criteria protective of the published migratory spawning, open- 
water, deep-water and deep-channel designated uses. These dissolved oxygen criteria include 30- 
day, 7-day and 1-day means along with instantaneous minima as needed to protect various 
species and life stages within the designated uses (U.S. EPA 2003). 

Since the Chesapeake Bay dissolved oxygen criteria were published in 2003, refinements and 
updates to the criteria attainment assessment methodologies have been published. Most recently, 
the refined and expanded dissolved oxygen criteria assessment methodologies documented in 
Chapter 3 and associated appendices of the Ambient Water Quality Criteria for Dissolved 
Oxygen, Water Clarity and Chlorophyll a for the Chesapeake Bay and its Tidal Tributaries - 
2008 Technical Support for Criteria Protocols Addendum , replaced the methodologies 
previously published by EPA (U.S. EPA 2008). 

Critical to the dissolved oxygen criteria assessments are the pycnocline delineations defining the 
timing and vertical position of the open-water, deep-water and deep-channel designated use 
boundaries. The standardized method for calculating upper and lower boundaries of pycnoclines 
was originally published in Ambient Water Quality Criteria for Dissolved Oxygen, Water Clarity 
and Chlorophyll a for the Chesapeake Bay and its Tidal Tributaries - 2004 Addendum (U.S. 
EPA 2004a). U.S. EPA (2008), on pages 15-18 together with its Appendix A, provide a review 
of, and step by step details associated with, calculating upper and lower pycnoclines which, in 
turn, delineate the vertical boundaries for the open-water, deep-water and deep-channel 
designated uses. 

The following outline lays out the assessment protocol steps for the 30-day mean criteria (open- 
water and deep-water dissolved oxygen criteria (see U.S. EPA 2008, Appendix A for details): 

1) Compiling and formatting the data set 

2) Interpolation of water quality monitoring data 

2.1 Vertical interpolation 

2.2 Horizontal interpolation 

2.3 30-day average interpolation by month 


8 


2.4 Apportioning results by designated use 

2.5 Water quality criteria assessment, attainment and violations 

Step 2.4 above, carried forward the Step 4-Pointwise Compliance considerations of a statistical 
decision-making framework originally published in U.S. EPA 2007a Chapter II: Refinements to 
Chesapeake Bay Water Quality Criteria Assessment Methodology (pp. 17-18) and revisited in 
U.S. EPA 2008 (Appendix A). This section on pointwise compliance states: 

“While interpolation allows for standardization of many types of data, pointwise 
attainment allows for standardization of many criteria. Because attainment is 
determined at moments in time and points in space, it is possible to vary the 
criterion in time and space. If different levels of a water quality criterion are 
acceptable in different seasons, then the criterion can vary seasonally. It is 
possible to implement different criteria over space for a segment that bridges, for 
example, oligohaline and mesohaline, salinity zones. It might even be possible to 
let the criterion be a continuous function of some ancillary variable such as 
temperature or salinity, although this situation requires that such data exist for 
every interpolator cell. The only requirement is that the final attainment 
determination be “yes” or “no” for each interpolator cell.” 

The implicit assumption of the Chesapeake Bay partners was that if no pycnoclines were found 
for a particular sampling event then the open-water designated use and its respective dissolved 
oxygen criteria were being applied, i.e. that water column dynamics including “episodic 
pycnoclines” were accounted for as part of the criteria assessment computations. The U.S. EPA 
Chesapeake Bay Program Office's criteria assessment computer code, however, applied the 
long-term average pycnocline depth(s) to those water quality monitoring cruise sampling events 
when no pycnocline was found for those 13 segments, identified in U.S. EPA 2004 where deep¬ 
water and/or deep channel designated uses applied during the June-September time period. 
Therefore, under special cases, on the basis of pre-determined characterization, there were errors 
in designated use classification. 

REVISING A PROCEDURAL ANOMALY IN THE DESIGNATED USE DELINEATION 
Identification of a Procedural Anomaly 

During 2009, a procedural anomaly was discovered between EPA published dissolved oxygen 
criteria assessment protocols through 2008 for pycnocline delineation that defined the boundaries 
for the open-water, deep-water and/or deep-channel designated uses and the assessment 
procedures as defined in the criteria assessment computer code developed by the EPA 
Chesapeake Bay Program Office and used by the states and the District. The published 
procedures set forth that attainment is determined at moments in time and space given that the 
designated uses, their boundaries and the applicable dissolved oxygen criteria will also vary in 
time and space (U.S. EPA 2003). U.S. EPA (2008) published details of the computations for 
identifying pycnoclines where they exist on a water quality monitoring cruise-by-cruise basis. 
EPA also identified 13 Chesapeake Bay segments where deep-water and (or) deep-channel 
designated uses applied during the June-September time period (U.S. EPA 2004, page 5, Figure 


9 





11-2, and Table 11-1 below). The remaining tidal segments in Chesapeake Bay were characterized 
as having the open-water designated use year-round. 


Table II-l Chesa 

peake Bay segments with assigned designated uses. 

Designated 

Use 

Segment Code 

Location 

Deep Water 
and Deep 
Channel 

CB3MH 

CB4MH 

CB5MH 

CHSMH 

EASMH 

PATMH 

POTMH 

RPPMH (portion S of UTM Y = 4185000) 

Chesapeake Bay Mainstem 
Chesapeake Bay Mainstem 
Chesapeake Bay Mainstem 

Chester River 

Eastern Bay 

Patapsco River 

Lower Potomac River 

Lower Rappahannock River 

Deep Water 
Only 

CB6PH (portion north of UTM Y 4145) 

CB7PH (portion N/NW of UTM Y = UTM X + 3752745) 
PAXMH 

SBEMH 

YRKPH 

Chesapeake Bay Mainstem 
Chesapeake Bay Mainstem 

Lower Patuxent River 

South Branch Elizabeth River 
Lower York River 


Source: U.S. EPA 2004 


The EPA Chesapeake Bay Program Office acknowledged this computation code improperly 
imposed pycnocline presence at times and places where none was found. Such applications of a 
long-term mean pycnocline instead of no pycnocline were, therefore, incorrectly applying 
dissolved oxygen criteria assessments in such situations. The EPA published procedures, as 
described below, allow for the presence of episodic pycnoclines. 

Episodic Pycnoclines Criteria Assessment Protocols Modification 

The dissolved oxygen criteria assessment methodology is now clarified to specifically allow the 
deep-water and deep-channel designated uses to occur “episodically” for those 13 segments that 
have been identified as having deep-water and (or) deep-channel designated uses (see Table II-1 
in U.S. EPA 2004) When a pycnocline is observed during the tidal water quality monitoring 
cruise within one of the 13 segments during June 1 through September 30, the deep-water and 
(or) deep-channel designated uses exist and their respective numeric dissolved oxygen criteria 
are applied to those uses. When no pycnocline is observed, the open-water designated use applies 
to the entire water column. By definition, this approach eliminates the default use of long term 
pycnocline average when no pycnocline is observed. 

Reassessment of previous dissolved oxygen assessments by EPA and its state and District 
partners showed only small changes in Chesapeake Bay dissolved oxygen criteria attainment 
results over time. Times and places where no pycnocline could be defined for summer season 
among the 13 Chesapeake Bay segments with previously defined deep-water and deep-channel 
designated uses were shown to be rare events. 


10 











EXPANDED APPLICATION OF DEEP-WATER AND DEEP-CHANNEL 

DESIGNATED USES 


A total of 13 Chesapeake Bay segments characterized with deep-water and deep-channel 
designated uses were published in U.S. EPA 2004 (Table II-1). In a number of segments 
classified as having the open-water designated use only applied year-round, dissolved oxygen 
criteria assessments through time provided evidence of persistent criteria non-attainment. In a 
select set of these same Chesapeake Bay segments, results from numerous Chesapeake Bay 
water quality/sediment transport model scenarios, simulating dissolved oxygen concentrations 
across a wide range of nutrient load reductions, suggested lack of dissolved oxygen responses to 
nutrient load reductions due to physical constraints to re-oxygenation. Segments not previously 
classified with the deep-water and (or) deep-channel designated uses in mesohaline salinities but 
showing both stratification (presence of a pycnocline) and persistent dissolved oxygen criteria 
non-attainment were reviewed for possible expanded application of deep-water and deep-channel 
designated uses. 

Review of Designated Use Definitions 

The 2003 Ambient Water Quality Criteria for Dissolved Oxygen , Water Clarity and Chlorophyll 
a for Chesapeake Bay and Its Tidal Tributaries highlights two relevant guidelines-stratification 
(presence of pycnoclines) and evidence of a physical barrier restricting reoxygenation-for 
determining the need to apply the deep-water and (or) deep-channel designated uses (U.S. EPA 
2003). Specifically, the following are published definitions for determining when and where the 
open-water, deep-water and (or) deep-channel designated uses apply within Chesapeake Bay 
tidal waters: 

Open-Water Designated Use 

“If the presence of a pycnocline prevents oxygen replenishment, the open-water 
fish and shellfish designated use extends only as far as the upper boundary of the 
pycnocline. If a pycnocline exists but other physical circulation patterns (such as 
the inflow of oxygen-rich oceanic bottom waters) provide oxygen replenishment 
to the deep waters, the open-water fish and shellfish designated use extends to the 
bottom water-sediment interface.” U.S. EPA 2003, Appendix A, page A-6. 

(Also see U.S. EPA 2007, pages 37-38, Dissolved oxygen assessments in shallow 
versus open waters, for details regarding the open water designated use definition 
beyond vertical water column structure.) 

Deep-Water Designated Use 

“Tidally influenced waters located between the measured depths of the upper and 
lower boundaries of the pycnocline, where a measured pycnocline is present and 
presents a barrier to oxygen replenishment from June 1 to September 30...the 
deep-water designated use extends from the upper boundary of the pycnocline 
down to the sediment/water interface at the bottom, where a lower boundary of 
the pycnocline is not calculated.” U.S. EPA 2003, Appendix A, page A-6. 


11 




Deep-Channel Designated Use 

“Tidally influenced waters at depths greater than the measured lower boundary of 
the pycnocline in isolated deep channels.” U.S. EPA 2003, Appendix A, page A- 
6 . 

Mesohaline Segments Expanded Designated Uses 

Using the time period 1991 -2000 1 , depth profiles of change in density and dissolved oxygen 
concentrations from the Chesapeake Bay Water Quality Monitoring Program 2 were reviewed for 
both evidence of stratification and prevention of re-oxygenation. Chesapeake Bay segments in 
the mesohaline salinity zone, not previously classified with deep-water and (or) deep-channel 
designated uses, were evaluated for evidence of stratification and persistent dissolved oxygen 
criteria non-attainment under a range of different Chesapeake Bay water quality/sediment 
transport model loading scenarios. Ten segments meeting these characteristics were identified in 
Maryland and Virginia's Chesapeake Bay tidal waters (Table 11-2). 

Table 11-2. Ten Chesapeake Bay segments in the mesohaline salinity zone of Maryland and 
Virginia’s Chesapeake Bay tidal waters reviewed for possible expanded designated use 
classifications. 


Chesapeake Bay Segment 

Tidal Water Body 

MAGMH 

Magothy River 

SOUMH 

South River 

EBEMH 

East Branch Elizabeth River 

WBEMH 

West Branch Elizabeth River 

CRRMH 

Corrottoman River 

FSBMH 

Fishing Bay 

WICMH 

Wicomico River 

SEVMH 

Severn River 

WSTMH 

West River 

YRKMH 

York River 


Only the South River (SOUMH) and Magothy River (MAGMH) segments met the deep-water 
designated use definition originally described in U.S. EPA 2003 where a measured pycnocline 
was present and presented a barrier to oxygen replenishment during the period June 1 to 
September 30. 

In the South River segment, 39 of 43 depth profiles (91%) had an upper pycnocline and 19 of 43 
depth profiles (44%) had a lower pycnocline. In the Magothy River, 16 of 40 depth profiles 
(40%) had an upper pycnocline and 0 of 40 depth profiles (0%) had a lower pycnocline. 
Evaluation of the Chesapeake Bay water quality/sediment transport model scenario results for 
both segments showed depression of dissolved oxygen concentrations with increasing depth 
suggesting a physical mixing constraint on re-oxygenation due to stratification. 


1 These years of Chesapeake Bay Water Quality Monitoring Program data were selected to be consistent with the 

hydrologic period for management application of the Chesapeake Bay Water Quality/Sediment Transport Model. 
: www.chesapeakebay.net 


12 







In the presence of a pycnocline, the deep-water designated use will also apply to the Magothy 
River and South River mesohaline segments in the June 1 through September 30 time period. 
The application of the deep-water designated use to these two segments is fully consistent with 
previously published procedures which called for: 

1. the physical exchange of higher oxygenated waters from the upper water-column is much 
reduced by density stratification, and 

2. pycnocline waters are not reoxygenated by riverine or oceanic bottom waters 
in order to apply the deep-water designated use (U.S. EPA 2003). 

Previously, such segments including the deep-water designated use were only thought to be 
"located principally in the river channel at the lower reaches of the major rivers and along the 
spine of the middle mainstem of the Bay” (U.S. EPA 2003). These analyses conducted in 
support of the development of this addendum have demonstrated the deep-water designated use 
can occur in smaller tidal tributaries segments receiving limited freshwater flow from their 
surrounding watershed. 

Given the South River segment has a lower pycnocline and 19 of 43 depth profiles (44%) over 
the 1991-2000 data record, consideration was given to whether a deep-channel designated use 
should apply to this segment as well as a deep-water designated use. The published procedures 
for delineating a deep-channel designated use included: 

1. The very deep water-column and adjacent bottom surficial sediment habitats located 
principally in the river channel at the lower reaches of the major river and along the spine 
of the middle mainstem of the bay; 

2. At depths below which seasonal anoxic to severe hypoxic conditions routinely set in and 
persist for extended periods of time under current conditions; and 

3. At depths greater than the lower boundary of the pycnocline (U.S. EPA 2003). 

The South River segment does not contain a "very deep water-column” given a total maximum 
depth of 5 meters and the segment does not have conditions where "seasonal anoxic to severe 
hypoxic conditions routinely set in and persist for extended periods of time under current 
conditions”. Therefore, even in the presence of a lower pycnocline, a deep-channel designated 
use will not be applied to this segment. 

The initial review of stratification and dissolved oxygen data from the eight remaining segments 
identified in Table 11-2 did not provide immediate evidence of where stratification appeared to be 
limiting oxygen replenishment. A more in-depth review of water column stratification conditions 
and identification of any needs for further adjustments to the applicable designated uses for the 
remaining segments is planned for completion prior to the 2012 303(d) listing cycle. 


13 



LITERATURE CITED 


U.S. Environmental Protection Agency. 2003. Ambient Water Quality Criteria for Dissolved 
Oxygen, Water Clarity and Chlorophyll a for Chesapeake Bay and Its Tidal Tributaries April 
2003 (Regional Criteria Guidance). EPA 903-R-03-002. Region 111 Chesapeake Bay Program 
Office, Annapolis, Maryland. 

U.S. Environmental Protection Agency. 2004. Technical Support Document for Identification of 
Chesapeake Bay Designated Uses and Attainability-2004 Addendum. October 2004. EPA 903-R- 
04-006, Chesapeake Bay Program Office, Annapolis, MD. 

U.S. Environmental Protection Agency. 2007. Ambient Water Quality Criteria for Dissolved 
Oxygen, Water Clarity and Chlorophyll a for the Chesapeake Bay and Its Tidal Tributaries — 

2007 Addendum. July 2007. EPA 903-R-07-003. Region III Chesapeake Bay Program Office, 
Annapolis, MD. 

U.S. Environmental Protection Agency. 2008. Ambient Water Quality Criteria for Dissolved 
Oxygen, Water Clarity and Chlorophyll a for the Chesapeake Bay and its Tidal Tributaries - 

2008 Technical Support for Criteria Protocols Addendum. September 2008. EPA 903-R-08-001. 
Region III Chesapeake Bay Program Office, Annapolis, MD. 


14 



CHAPTER 3 


Biologically-based Reference Curves: Revisions to the 

Methodology and Applications 

BACKGROUND 

The published dissolved oxygen criteria assessment methodology currently used for assessing 
Chesapeake Bay water quality criteria attainment involves the use of cumulative frequency 
distribution (CFD) curves in a two-dimensional space of percent time and percent space (U.S. 
EPA 2003). Minimum concentrations of dissolved oxygen must be present to support species and 
their various life stages requiring protection. Dissolved oxygen criteria provide threshold 
conditions established for the designated uses such that water quality conditions that exceed this 
threshold are considered impaired. 

However, it is recognized that all water quality parameters are inherently variable in space and 
time. There will be small regions that persistently exceed the threshold due to poor flushing or 
other natural conditions. The Chesapeake Bay dissolved oxygen criteria have several durations 
reflecting the various tolerances of different life stages and effects (U.S. EPA 2003, 2008). Small 
regions or time periods of degraded condition should not lead to a degraded assessment for the 
segment (U.S. EPA 2003). Recognition that ephemeral exceedances of the threshold in both time 
and space do not represent persistent impairment of the segment leads to an assessment 
methodology that allows these conditions to be classed as acceptable while conditions of 
persistent and wide spread impaired condition will be flagged as unacceptable. (E. Perry, Pers. 
Comm. 2005). 

During an independent scientific peer review of the EPA published CFD procedures, reviewers 
raised specific concerns about the method for deriving the biological reference curves (STAC 
2006). At the time, there were no apparent solutions to resolve the concerns that were raised. 
However, during recent application of criteria assessment procedures to model simulated 
outputs, evaluation of the resultant model outputs put the spotlight back on the criteria 
assessment process and the underlying biological reference curve methodology. 

Work by the EPA Chesapeake Bay Program Office and its partners suggested that application of 
the currently published application of the Benthic-Index of Biotic Integrity (B-IBI) (Weisberg et 
al. 1997) did not accurately distinguish between healthy and degraded communities with 
corresponding distinct sets of dissolved oxygen violations. EPA Chesapeake Bay Program Office 
analysts and partners worked with recognized Chesapeake Bay benthic community experts 2 to 
revise the published methods for identifying “healthy” and “degraded” benthic communities. 
During this process, it was determined that the B-IBI provides a robust delineation of healthy and 
degraded benthic communities with corresponding distinct dissolved oxygen violation rates. 


2 Dr. Dan Dauer, Old Dominion University and Dr. Roberto Llanso, Versar, Inc. 



Using the newly delineated “healthy” and “degraded” benthic communities, EPA Chesapeake 
Bay Program Office analysts worked to produce a set of revised biological reference curves that 
minimize the error in distinguishing between “healthy” and “degraded" segments. In this chapter 
and its associated appendices, updates to the methodology involving development of 
biologically-based reference curves with Chesapeake Bay benthic macroinvertebrate monitoring 
program data are provided. Further, directions on application of reference curves for open-water, 
deep-water and deep-channel designated uses are provided for completing the Chesapeake Bay 
dissolved oxygen criteria attainment computations. 

ISSUES WITH DISSOLVED OXYGEN CRITERIA ASSESSMENT WITH THE 
PREVIOUSLY PUBLISHED BIOLOGICALLY-BASED REFERENCE CURVES 

The current published method for assessing dissolved oxygen (DO) impairments in Chesapeake 
Bay incorporates the use of a cumulative frequency distribution as the final step of assessment 
(U.S. EPA 2003). In this step, a set of DO violation rates for a particular segment-designated use 
(e.g. “CB4MH Deep Water”) are plotted as a cumulative frequency distribution (CFD) and 
compared to a “biological reference curve” comprising a cumulative frequency distribution of 
“acceptable violation rates” of the DO criteria. If the assessment curve exceeds, at any point , the 
reference CFD, then the given segment is considered “impaired (Figure III-1). 



Figure III-l. Conceptual graph illustrating the CFD assessment procedure. The red line is an 
example of a hypothetical “healthy” assessment curve; the blue line is the hypothetical reference 
curve. 

It has been recognized, however, that by combining violation rates from all healthy areas into 
one biologically-based reference curve, we create a curve that theoretically represents 
approximately the median of all curves included. Thus, a large percentage of the presumably 
“acceptable” violation rate CFDs that were pooled in order to generate the biologically-based 
reference curve may fail an assessment conducted against that same biologically-based reference 
curve. A more detailed evaluation confirmed this concern. In Figure III-2 below, the CFD for 


16 






CB3MH Deep Water 1987, a segment/designated use considered having a healthy B-1BI for that 
year, whose acceptable violation rates were included in the generation of the biological reference 
curve, fails assessment by that same biological reference curve. 



Figure III-2. An example of a 30-day mean deep-water dissolved oxygen criteria and the 
violation expressed by a healthy segment (CB3MH 1987) curve used in deriving the 30-day 
mean criterion biologically-based reference curve. 

Further analyses revealed that the biological reference curves used for the deep-water and deep- 
channel dissolved oxygen criteria attainment assessments fail the majority of supposedly 
“healthy” segment-years used to construct those same curves. 

As described in U.S. EPA 2003, the preferred methodology for defining the reference curve is to 
determine levels of allowable violation based on the demonstrated tolerance of the living 
resources for whose protection the water quality criteria were designed. Benthic habitat 
assessments were conducted with the updated methodology, which is described below, for 
assessing the appropriateness of biologically-based reference curves as indicators of water 
quality conditions. 


UPDATES TO DISSOLVED OXYGEN BIOLOGICALLY-BASED REFERENCE 

CURVE DERIVATION METHODOLOGY 

Based on the findings described above, the following revisions are recommended to the 
methodology for categorizing benthic communities as “healthy” for the purposes of providing a 
reference for allowable frequency of dissolved oxygen criteria exceedance. The intent of these 
revisions is to improve the accuracy with which benthic communities are categorized as healthy. 

Revisions to the previously published methodology for developing dissolved oxygen biological 
reference curves include: 

1) Restriction of the reference dataset to data collected beginning in 1996; 

2) expansion of time period for classifying benthic community health from 1 year to 
sequential 3-year time periods; 


17 








3) restriction of reference segment-periods to those for which at least 10 observations are 
available; 

4) refined definition of a “healthy” benthic community as one for which the mean B-IB1 
score is at least 3.0; 

5) the standard deviation of the mean is less than 1.0; and 

6) use Grand Score in computations involving fixed data. 

The rationale underlying each of these six modifications is described in further detail below. 

Restrict Dataset to Data Collected Beginning in 1996 

Criteria violation results of dissolved oxygen criteria attainment assessments are compared with 
a reference CFD curve (e.g., standard 10% reference or biologically-based reference CFD curve), 
representing allowable amounts of criteria exceedance in a healthy habitat. When an appropriate 
biological reference community is identified and sufficient data are deemed available, a 
biological reference curve of acceptable percent exceedance is generated using a CFD of 
violation rates for “healthy” biological communities in that designated use. A review of the 
plotting methodology is provided in U.S. EPA 2008 (see Appendix A). 

Historically, the benthic monitoring work of the Chesapeake Bay Benthic Monitoring Program 
consisted of fixed station monitoring with sampling usually taking place in August and 
September (Chesapeake Bay Program 1989). The sampling design was primarily intended to 
assess long-term trends in living resources over decadal, annual and seasonal time scales. 

Derivation of the original dissolved oxygen biologically-based reference curves relied on the 
1985-2005 Chesapeake Bay benthic monitoring program dataset in order to take advantage of the 
full two decades of monitoring results. However, data collection methods have undergone 
revision during the 21 years of monitoring. In 1996, a stratified random sampling component was 
added to the benthic monitoring program in order to provide confidence limits on estimates of 
impaired waters in Chesapeake Bay. In order to ensure adequate spatial resolution of benthic 
community health, STAC (2009), in accordance with recognized Chesapeake Bay benthic 
community experts, recommended truncating the reference data set to start in 1996 when the 
updated sampling procedures were established. The data period was extended one year to 2006 
to include the most recently available data. The use of the 1996-2006 Chesapeake Bay benthic 
monitoring program data set is an update to previously published methods (U.S. EPA 2007, 
Chapter 4). The recommended data set represents a consistent period of improved assessments of 
Chesapeake Bay health condition. 

Use Sequential 3-year Time Periods Rather Than Single Years 

The biologically-based reference curve derivation methodology, as outlined in U.S. EPA 2007 
(see Chapter 4), used single year assessments to determine the health of the benthic community 
for the purposes of identifying acceptable dissolved oxygen criteria exceedances. However, 
dissolved oxygen criteria assessments are conducted on sequential 3-year time frames for each 
segment (U.S. EPA 2003); two year time steps are used in reporting for 303d listing cycles (e.g. 
the 2008 303d listing cycle used 2004-2006 data, the 2010 303d listing cycle used 2006-2008 


18 


data) while benthic community assessments are conducted annually with annual time steps for a 
variety of purposes (e.g. indicator reporting for the Chesapeake Bay Barometer). Using 
sequential 3-year time periods to classify benthic community health, advancing the data in one 
year time steps (e.g. 1996-1998, 1997-1999, etc.), brings the reference community identification 
method into better alignment with the dissolved oxygen criteria assessment protocols for which 
reference communities are being identified. This modification addresses a concern raised by the 
Chesapeake Bay Program's Scientific and Technical Advisory Committee (STAC) review of the 
CFD approach (STAC 2006) which noted that sample sizes for reference and assessed conditions 
should be made similar to reduce the effect of sample size bias on the shape of the CFD. The 
combination of a segment and sequential 3-year assessment time periods is hereafter referred to 
as a “segment period”. 

Screening criteria: Sample Size > 10 

Keller and Cavallaro (2008) reported that listing decisions on the U.S. Clean Water Act 303a 
listing impairments of surface waters by states were often based on insufficient data, or that data 
were not sufficiently representative of temporal and spatial conditions for the water body being 
assessed. Llanso et al. (2009), however, require a minimum sample size of n > 10 for habitat 
health assessments using the Chesapeake Bay B-IB1. The EPA Chesapeake Bay Program Office 
and its partners examined the effects of relaxing the data screening criteria to accept segment- 
period combinations with sample size > 8 to increase the number of “healthy” segment-periods 
available for reference community analysis. 

The decision to eliminate segment-periods with fewer than 10 observations was based on 
analyses by EPA Chesapeake Bay Program Office and its partners, which showed that fewer 
than 10 observations weakened the ability of the reference CFD to appropriately classify 
segments. Llanso et al (2009) confirmed Keller and Cavallaro (2008)’s findings regarding 
sample size and temporal and spatial distribution. They found that analysis of Chesapeake Bay 
segments with less than 10 samples produced “inconclusive results relative to the (U.S. EPA) 
listing process.” In their review of the proposed methodology, STAC (2009) determined that a 
minimum sample size of 10 is reasonable and has been applied elsewhere (Alden et al. 2002). 
Further details on the sample size analyses are available in Appendix A. 

Screening Criteria: Standard Deviation <1.0 

The EPA Chesapeake Bay Program Office and its partners examined the isolated and combined 
effects of relaxing the data screening criteria to accept segment-periods with fewer samples (n > 
8 instead of 10) and/or expanding the standard deviation criteria surrounding the B-IBI results 
from <1.0 to < 1.2 in order to increase the number of “healthy” segment-periods for analysis. 
The relaxation of both the sample size and the standard deviation criteria (see Scenario D in 
Appendix A) increases the number of segment-periods classified as “healthy” from 10 to 16. 
Flowever, four of these additional CFD curves extend into “degraded” CFD space to a degree 
that calls into question the accuracy of their classification as healthy (see Figure A-3 in 
Appendix A). Defining healthy benthic communities for deriving a benthic community based 
biological reference curve, therefore, relies on sample size n > 10 with a standard deviation < 


19 


1.0. Further details of the sample size and standard deviation analyses are available in Appendix 

A. 

Definition of Healthy Benthic Macroinvertebrate Reference Community Conditions 

The methodology described by U.S. EPA (2007, 2008) defined healthy segments (with respect to 
benthic communities) as those with a minimum B-1B1 score > 3.0. However, no sample size 
restriction was introduced. As a result, a large segment could contain a single B-1BI score, and if 
that single score exceeded 3, then the segment was classified as healthy. The likelihood of a 
degraded segment containing 10 B-1BI scores (in any given 3 years) all of which are > 3.0 is 
small. Furthermore, benthic community experts (Llanso et al. 2009) have more commonly 
defined a healthy community as one with a sample mean > 3.0, given an adequately large sample 
size and small variance. Thus, the EPA Chesapeake Bay Program Office and its partners now 
define '‘healthy” benthic reference communities as those with an average B-IBI score > 3.0 and 
standard deviation (SD) < 1.0. STAC (2009) supported the use of “healthy” benthic reference 
communities defined by those with an average B-IBI score > 3.0, rather than a minimum, and a 
standard deviation (SD) < 1.0, (n > 10). A degraded benthic community is defined as having an 
average B-IBI score <3.0 with a standard deviation < 1.0, (n > 10). 

The methodological refinements described above led to findings that provide ongoing support of 
the need for a hyperbolic curve that distributes allowable violations in CFD space, as do both the 
new deep-water biologically-based reference curve described below and the default 10% 
reference curve described in U.S. EPA (2007). A more in-depth discussion of the shape of the 
reference curve with respect to “healthy” and “degraded” CFD-space can be found in Appendix 

B. 

STAC (2009) recommendations suggested that based on the assumptions of normality, the 
standard deviation criterion applied when classifying a healthy benthic community could 
alternatively be expressed as “no more than 16% of the sample observations should have a score 
less than 2.0”. This is a one-sided version of the screening criterion, and addresses concerns that 
clearly healthy segments with high variance could be excluded from the analyses. EPA 
Chesapeake Bay Program Office staff conducted an exploratory analysis to classify benthic 
communities using the following benthic community classification rules: 

1) average B-IBI score > 3.0 with no more than 16% of sample observations < 2.0 (n > 10) 
defines a healthy benthic community, and 

2) average B-IBI score < 3.0 with no more 16% of sample observations > 4.0 B-IBI score, 
(n > 10) defines a degraded benthic community. 

Results using these revised classification rules were consistent with the results of the 
biologically-based reference curve derivation methodology outlined in this chapter. 

Use Grand Score in Computations Involving Fixed Station Data 

The 1996-2006 Chesapeake Bay B-IBI sample results consist of both fixed station and random 
station data. These data are combined in the analyses but have different scoring categories within 
the CIMS database. 


20 


Specifically, for the “fixed station" samples both “total_score" and “grand_score" records are 
reported within the Chesapeake Bay Information Management System (C1MS) 3 . "Totalscore" 
records are replicate measurements of the same community event; the average of these is 
reported as the “grand score." The Chesapeake Bay benthic experts (R. Llanso, Versar Inc., 
Pers. Comm. 2009) recommended using the “grand score" in the Chesapeake Bay dissolved 
oxygen criteria assessment analyses to avoid errors not accounting for the replicate results of a 
sampling event. By comparison, random station records in the CIMS database report only a 
“total score" as the sampling event B-1BI measure; no “grand scores” will be found associated 
with random station data records. 


SUMMARY OF RECOMMENDATIONS 

Based on the findings of the analyses and in accordance with the STAC (2009) 
recommendations. Table III-l summarizes the revisions to the methodology for identifying 
dissolved oxygen biologically-based reference curves for Chesapeake Bay water quality criteria 
attainment assessments (Table III-l). 


21 


Table III-l. Chesapeake Bay dissolved oxygen criteria biologically-based reference curve 
derivation recommendations. 


U.S. EPA 2007, 2008 Addenda 

2010 Addendum 

Obtain dataset of all benthic index of biotic integrity (B-IBI) scores for 
time period 1985-2005 

Restrict dataset to data starting in 

1996; for random station data use 
‘total score’ and for fixed station 
samples use “grand score” only. 1 

For the relevant subset of Chesapeake Bay segments with open-water 
(OW) and deep-water (DW) and/or deep-channel (DC) designated uses: 


Match benthic stations and scores in a dataset with monthly open-water, 
deep-water, and deep-channel designated use boundaries. 


• Boundaries are derived using the standardized, automated 
method for identifying pycnocline boundaries documented in 
U.S. EPA 2008. 

Pycnocline boundaries are 
interpolated using the episodic 
pycnoclines approach defined in 
Chapter 2, this addendum. 

Pycnocline boundaries are then interpolated using the interpolator 
(Visual Basic program, Version 4.61, August 2006, Chesapeake Bay 
Program Office, as referenced in U.S. EPA 2008, Appendix A, p36). 


• Interpolator cells are matched with benthic station locations, and 
interpolated pycnocline boundaries are applied to each benthic 
station location. 


Benthic stations (and their associated B-IBI scores) are assigned to a 
designated use: OW, DW, or DC. 

No modification recommended 

To define the biological reference community for each designated use, all 
individual segment-years for which the minimum B-IBI was > 3.0 are 
identified. (Minimum sample size within a segment-year is recognized as 
n=l.) These are denoted as ‘healthy’ segment-years. 

a. Use 3-year rolling time periods 
rather than single years. 2 

b. Require a B-IBI score sample 
size n _> 10. 3 

C. “Healthy” reference 

communities are those with an 
average B-IBI score > 3.0 rather 
than a minimum, and standard 
deviation (SD) < 1,0. 4 

For the ‘healthy’ segment-years, the monthly (in the case of OW and 
DW) or instantaneous (DC) dissolved oxygen criteria violation rates are 
obtained based on the water quality profiles of sampling data collected by 
the Chesapeake Bay long term water quality monitoring program. 

No modification recommended. 

These season- and designated use-specific Chesapeake Bay dissolved 
oxygen criteria violation rates (e.g. percentage of a segment-designated 
use volumes failing the DO criteria in a given month; thus 4 measures 
per summer for OW and DW - June thru September) are used to define 
“acceptable” exceedances of the dissolved oxygen criteria. This 
definition of acceptable exceedances in space and time is based on the 
logic that if a healthy benthic community existed in the segment- 
designated use in that summer, then the degree of DO criteria violation 
that occurred did not lead to an impaired benthic community. 

No modification recommended. 




Source: U.S. EPA 2003, 2007, 2008. 


22 
















1 . 


Restrict dataset to 1996-2006 time period. For the fixed station samples included in the analyses, use the “grand 
score” only from the CIMS data base with these samples. 

2. Use 3-year rolling time periods rather than single years. This brings the reference community ID method into 
better alignment with the DO criteria assessment method for which reference communities are being identified. 

3. Require a B-IBI score sample size > 10. This improves the spatial representation of the B-IBI score. 

4. “Healthy” reference communities are those with an average B-IBI score > 3.0, and a standard deviation (SD) < 
1.0, rather than a minimum. Using the average is consistent with published methods used by Chesapeake 
benthic experts to assess benthic communities (e.g. Llanso et al. 2009). 

APPLICATION OF A REFERENCE CURVE FOR OPEN-WATER 30-DAY MEAN 
DISSOLVED OXYGEN CRITERIA: SUMMER SEASON 

Reference curves for the 30-day mean open-water dissolved oxygen criterion (June 1-September 
30 only) were based on criteria levels that would not impair biological communities (U.S. EPA 
2003). Analyses conducted by the EPA Chesapeake Bay Program Office and its partners suggest 
that the B-IBI does not provide an appropriate reference community for assessment of open- 
water dissolved oxygen criteria violations. Even with the latest improvements in the assessment 
methodology to distinguish between healthy and degraded benthic communities, Figure III-3 
illustrates that the health of the benthic community is not an appropriate indicator of open-water 
low dissolved oxygen conditions as defined by the summer season open-water 30-day mean 
dissolved oxygen criterion. This result is demonstrated by the cloudplot (Figure III-3) 
representing Chesapeake Bay Program segments deemed “healthy” and “degraded” according 
the updated assessment methodology. 



Figure III-3. Open water “healthy” and “degraded” benthic communities are not distinguished 
by violations of the summer open water DO 30-day mean criterion 

APPLICATION OF A REFERENCE CURVE FOR DEEP-WATER MEAN DISSOLVED 

OXYGEN CRITERIA 


Reference curves for the 30-day mean deep-water dissolved oxygen criteria (June 1-September 
30 only) were based on criteria levels that would not impair biological communities (U.S. EPA 
2003). Reference areas for derivation of the original 2003 published deep-water biologically- 












Table 111-1 . Chesapeake Bay dissolved oxygen criteria biologically-based reference curve 


derivation recommendations. 


U.S. EPA 2007, 2008 Addenda 

2010 Addendum 

Obtain dataset of all benthic index of biotic integrity (B-1BI) scores for 
time period 1985-2005 

Restrict dataset to data starting in 

1996; for random station data use 
‘total score’ and for fixed station 
samples use “grand score” only. 1 

For the relevant subset of Chesapeake Bay segments with open-water 
(OW) and deep-water (DW) and/or deep-channel (DC) designated uses: 

Match benthic stations and scores in a dataset with monthly open-water, 
deep-water, and deep-channel designated use boundaries. 

• Boundaries are derived using the standardized, automated 
method for identifying pycnocline boundaries documented in 
U.S. EPA 2008. 

Pycnocline boundaries are then interpolated using the interpolator 
(Visual Basic program. Version 4.61, August 2006, Chesapeake Bay 
Program Office, as referenced in U.S. EPA 2008, Appendix A, p36). 

• Interpolator cells are matched with benthic station locations, and 
interpolated pycnocline boundaries are applied to each benthic 
station location. 

Pycnocline boundaries are 
interpolated using the episodic 
pycnoclines approach defined in 
Chapter 2, this addendum. 

Benthic stations (and their associated B-IB1 scores) are assigned to a 
designated use: OW, DW, or DC. 

No modification recommended 

To define the biological reference community for each designated use, all 
individual segment-years for which the minimum B-IBI was > 3.0 are 
identified. (Minimum sample size within a segment-year is recognized as 
n=l.) These are denoted as ‘healthy’ segment-years. 

a. Use 3-year rolling time periods 
rather than single years.' 

b. Require a B-IBI score sample 
size n _> 10. 3 

C. “Healthy” reference 

communities are those with an 
average B-IBI score > 3.0 rather 
than a minimum, and standard 
deviation (SD) < 1,0. 4 

For the ‘healthy’ segment-years, the monthly (in the case of OW and 
DW) or instantaneous (DC) dissolved oxygen criteria violation rates are 
obtained based on the water quality profiles of sampling data collected by 
the Chesapeake Bay long term water quality monitoring program. 

No modification recommended. 

These season- and designated use-specific Chesapeake Bay dissolved 

oxygen criteria violation rates (e.g. percentage of a segment-designated 
use volumes failing the DO criteria in a given month; thus 4 measures 
per summer for OW and DW - June thru September) are used to define 
“acceptable” exceedances of the dissolved oxygen criteria. This 
definition of acceptable exceedances in space and time is based on the 
logic that if a healthy benthic community existed in the segment- 
designated use in that summer, then the degree of DO criteria violation 
that occurred did not lead to an impaired benthic community. 

No modification recommended. 


Source: U.S. EPA 2003, 2007, 2008. 












1 . 


Restrict dataset to 1996-2006 time period. For the Fixed station samples included in the analyses, use the “grand 
score” only from the CIMS data base with these samples. 

2. Use 3-year rolling time periods rather than single years. This brings the reference community ID method into 
better alignment with the DO criteria assessment method for which reference communities are being identified. 

3. Require a B-1B1 score sample size > 10. This improves the spatial representation of the B-1BI score. 

4. “Healthy” reference communities are those with an average B-IBI score > 3.0, and a standard deviation (SD) < 
1.0, rather than a minimum. Using the average is consistent with published methods used by Chesapeake 
benthic experts to assess benthic communities (e.g. Llanso et al. 2009). 

APPLICATION OF A REFERENCE CURVE FOR OPEN-WATER 30-DAY MEAN 
DISSOLVED OXYGEN CRITERIA: SUMMER SEASON 

Reference curves for the 30-day mean open-water dissolved oxygen criterion (June 1-September 
30 only) were based on criteria levels that would not impair biological communities (U.S. EPA 
2003). Analyses conducted by the EPA Chesapeake Bay Program Office and its partners suggest 
that the B-IBI does not provide an appropriate reference community for assessment of open- 
water dissolved oxygen criteria violations. Even with the latest improvements in the assessment 
methodology to distinguish between healthy and degraded benthic communities, Figure III-3 
illustrates that the health of the benthic community is not an appropriate indicator of open-water 
low dissolved oxygen conditions as defined by the summer season open-water 30-day mean 
dissolved oxygen criterion. This result is demonstrated by the cloudplot (Figure III-3) 
representing Chesapeake Bay Program segments deemed “healthy” and “degraded” according 
the updated assessment methodology. 


! 



Figure III-3. Open water “healthy” and “degraded” benthic communities are not distinguished 
by violations of the summer open water DO 30-day mean criterion 

APPLICATION OF A REFERENCE CURVE FOR DEEP-WATER MEAN DISSOLVED 

OXYGEN CRITERIA 

Reference curves for the 30-day mean deep-water dissolved oxygen criteria (June 1-September 
30 only) were based on criteria levels that would not impair biological communities (U.S. EPA 
2003). Reference areas for derivation of the original 2003 published deep-water biologically- 


23 













based reference curves were identified using a measure of benthic community health - the 
Chesapeake Bay B-IBI (Weisburg et al. 1997). Using the revised methodology outlined in this 
addendum chapter, the EPA Chesapeake Bay Program Office and its partners identified two 
distinct sets of “healthy” and “degraded” (average B-IBI < 3.0, SD < 1.0) benthic communities, 
with correspondingly distinct violation rates (Figure III-4). The EPA Chesapeake Bay Program 
Office, in coordination with its partners, further determined that a reference curve constructed 
from the 100 lh percentile of healthy violation rates (x) for each point in time (y) accurately 
distinguished between healthy and degraded benthic communities with zero error in 
classification. 

A step-by-step guide to the derivation of this curve (Figure III-4), including the x-y coordinate 
values for plotting the curve, is provided in Appendix C. 








—*- r.RRPH 1999 ?ooi 









-•— POTM HI 9987000 












space 

Figure III-4. Dissolved Oxygen deep-water criteria violation rates corresponding to healthy 
(blue) and degraded (red) benthic communities. Recommended new deep-water biologically- 
based reference curve represented by the 100 th percentile of healthy violations is shown in black. 

APPLICATION OF A REFERENCE CURVE FOR DEEP-CHANNEL 
INSTANTANEOUS MINIMUM DISSOLVED OXYGEN CRITERIA 

In the case of the deep-channel instantaneous minimum dissolved oxygen criterion, the 
application of a biological reference curve was recommended in U.S. EPA 2007 (p. 43). 
Appendix D provides a more thorough review of history of EPA guidance regarding application 
of the deep-channel reference curve. 


This 2007 recommendation for application of a biologically-based reference curve for 
assessment of the deep-channel dissolved oxygen criterion was based on the identification of a 


24 



































small number of deep-channel segment-periods within which the benthic communities were 
categorized as “healthy" and, therefore, appropriate for use as a biological reference. These 
benthic communities were categorized using the methodology described on pp. 39-41 of U.S. 
EPA 2007. 

The revised methodology published in this addendum was applied to derive a new deep-channel 
biologically-based reference curve. The revised method yielded no segment-periods meeting the 
revised criteria outlined in Table III-1 above. This suggests that the occurrence of healthy 
benthic communities in the deep-channel designated use are currently insufficient to identify a 
corresponding set of “acceptable" violations of the instantaneous minimum dissolved oxygen 
criteria to develop a biologically-based reference curve. 

Comparisons of Degraded Reference Benthic Communities with the Published Deep- 
Channel Reference Curve 

While no benthic communities could be categorized as “healthy” in the most recent review, 25 
“degraded" reference benthic community segment-periods were identified. The EPA 
Chesapeake Bay Program Office and its partners conducted and reviewed analyses that showed 
that all 25 segment-periods (in the 1996-2005 time period) for which deep-channel benthic 
communities were categorized as “degraded" failed a dissolved oxygen criteria assessment 
conducted using the 10% default reference curve (Figure III-5). 


i 


0.8 


0.6 


E 


0.4 


0.2 



space 

Figure III-5. CFD graph of deep-channel instantaneous minimum dissolved oxygen criterion 
violation rates corresponding to benthic communities categorized as “degraded" (red lines) in 
relation to the 10% default reference curve (blue line). 

In the absence of a suitable reference community, a biological reference curve for the deep- 
channel instantaneous minimum dissolved oxygen criterion can not be constructed at this time. 
Under these circumstances, “a default reference curve such as the normal distribution curve 


25 





















representing approximately 10 percent exceedance is appropriate in this case to account for 
anticipated natural criteria exceedances” (U.S. EPA 2003; p. 173). 

Rationale for Acceptable Exceedances of the Deep Channel Instantaneous Minimum 
Dissolved Oxygen Criterion 

EPA determined that there are allowable criteria exceedances that would not adversely effect 
protection of the designated use. As documented on p. 168 in U.S. EPA 2003: 

“The recommended criteria attainment assessment approach is designed to 
protect the living resources as defined by the designated uses. The criteria levels 
themselves were largely based on scientific studies performed in laboratory 
settings or under controlled field conditions. The criteria establish the level of a 
given habitat condition that living resources need for survival. They do not 
account for many other environmental factors that could affect survival. 

Reference curves were developed to provide a scientific-based, direct measure 
of the ‘allowable' criteria exceedances. These exceedances are defined to be 
those that last a short enough time or cover a small enough area to have no 
adverse affects on the designated use. It is assumed that the designated uses can 
be attained even with some limited level of criteria exceedances and thus, the 
reference curves define those criteria exceedances deemed to be allowable— 
chronic in time but over small areas, or infrequent occurrences over large areas. 
Exceedances that occur over large areas of space and time would be expected to 
have significant detrimental effects on biological communities, which would 
imply nonattainment of designated uses.” 

As reported in a recent paper on the Chesapeake Bay dissolved oxygen criteria by the key 
members of the original Chesapeake Bay dissolved oxygen (DO) criteria team (Batiuk et al. 
2009): 


“Unlike chemical contaminants or other more conventional pollutants, there 
were no clear, well established guidelines for deriving criteria for DO, 
particularly for estuarine waters inhabited by fresh-water and marine species. 
The goal in setting Chesapeake DO criteria was to use the best science possible 
to define conditions that would improve or sustain the suitability of Chesapeake 
Bay habitats for finfish and invertebrates, with the states ultimately factoring in 
consideration of attainability in adopting the criteria as water quality standards. 
Thus, we developed criteria that would greatly increase the spatial and temporal 
extent of Bay waters in which oxygen concentrations were not major limitations 
to growth and survival of organisms dependent on particular Bay habitats. We 
did not, however, derive criteria that would require oxygen concentrations high 
enough at all times and in all locations such that no organism would be 
negatively affected in any location in the Bay. The states and U.S. 
Environmental Protection Agency (EPA) determined that such conditions would 
not be achievable either economically nor technologically (U.S. EPA, 2003d) 
and may not, in fact, reflect pre-historical conditions of Chesapeake Bay, which 


26 


showed that low oxygen conditions, although not nearly as severe as today, may 
have been a historical feature in the deep channel of the bay (Cooper and 
Brush, 1991; Karlsen et al., 2000; Adelson et ah, 2001; Zimmerman and Canuel, 

2002; Bratton et ah, 2003; Colman and Bratton, 2003; Cronin and Vann, 2003; 

Zheng et ah, 2003).” 

In support of the deep-channel instantaneous minimum criterion of 1 mg/L, U.S. EPA 2003 
summarized findings published in peer-reviewed literature sources indicating that several 
keystone benthic species “are resistant to dissolved oxygen concentrations as low as 0.6 mg/L,” 
and that “extensive mortality is likely only under persistent exposure to very low dissolved 
oxygen concentrations at high summer temperatures” (p. 61). 

In light of both (1) the recognition that low dissolved oxygen conditions are a ‘pre-historical’ 
feature of these deep channel habitats, and (2) the observation that keystone benthic species of 
these deep channel habitats can tolerate small-scale occurrences of severe hypoxia (DO 
concentrations below 1 mg/L), EPA believes that an allowance for a small, limited set of 
exceedances in time and space is acceptable in assessment of the deep-channel designated use 
dissolved oxygen criterion. 

ASSESSMENT OF SUMMER SEASON DISSOLVED OXYGEN CRITERIA 

EPA recommends revising previously published dissolved oxygen criteria assessment guidance 
as described in Table 111-2, including applying the default 10% reference curve for assessment of 
summer season (June 1- September 30) 30-day mean open-water and instantaneous minimum 
deep-channel dissolved oxygen criteria. The 30-day mean deep-water dissolved oxygen criterion 
biologically-based reference curve, as described in this addendum, is recommended for use 
assessing attainment of this criterion. Until EPA publishes methodologies for assessing the 7-day 
mean, 1-day mean and instantaneous minimum open-water and deep-water dissolved oxygen 
criteria, respectively, the Agency recommends that the states and the District of Columbia rely 
strictly on the assessment of the 30-day mean open-water and deep-water dissolved oxygen 
criteria for listing decisions (U.S. EPA 2007). The previously published non-summer open-water 
dissolved oxygen criteria reference curve remains unchanged as the 10% default reference curve 
(U.S. EPA 2007, p.42). 


27 


Table III-2. EPA recommended reference curves for conducting 303(d) list Chesapeake Bay 
dissolved oxygen criteria assessments. __ 


Season and Designated 
Use 

U.S. EPA 2007 July Addendum 
Reference Curve 

U.S. EPA 2010 Addendum 
Reference Curve 

Summer Open Water 
(30-day mean) 

Published biologically-based 
reference curve. 

Published default 10% 
reference curve 


Refer to U.S. EPA 2007 
p. 41, Figure IV-2. 

Refer to U.S. EPA 2007, pi3, 
Figure II-4 and Equation 1. 

Non-summer Open Water 
(30-day mean) 

Published default 10% reference 

curve. 

Published default 10% 
reference curve 


Refer to U.S. EPA 2007, 

p. 13, Figure II-4 and Equation 1. 

Refer to U.S. EPA July 2007, 
p.13, Figure 11-4 and Equation 

1 . 

Summer Deep Water 
(30-day mean) 

Published biologically-based 
reference curve. 

Refer to U.S. EPA 2007, 
p. 41, Figure IV-3. 

Revised Biologically-based 
reference curve. Figure III.4, 
and Appendix C. this 
document. 

Summer Deep Channel 
(instantaneous minimum) 

Published Biologically-based 
reference curve. 

Published default 10% 
reference curve 


Refer to U.S. EPA 2007 

p. 42 Figure IV-4 and Appendix F 

and G. 

Refer to U.S. EPA 2007, pi3, 
Figure II-4 and Equation 1. 


Sources: U.S. EPA 2003, 2007. 


LITERATURE CITED 

Adelson, J. M., G. R. Helz and C. V. Miller. 2000. Reconstructing the rise of recent coastal 
anoxia; molybdenum in Chesapeake Bay sediments. Geochemica et Cosmochemica Acta 
65:237-252. 

Alden III, R.A., D.M. Dauer, J.A. Ranasinghe, L.C. Scott, and R.J. Llanso. 2002. Statistical 
verification of the Chesapeake Bay benthic index of biotic integrity. Environmetrics 13:473-498. 

Bratton, J. F., S. M. Colman, R. R. Seal and P. C. Baucom. 2003.In press. Eutrophication and 
carbon sources in Chesapeake Bay over the last 2,700 years: Human impacts in context. 
Geochimica et Cosmochimica Acta. 

Batiuk, R.A., D.L. Breitburg, R.J. Diaz, T.M. Cronin, D.H. Secor and G. Thursby. 2009. 
Derivation of habitat-specific dissolved oxygen criteria for Chesapeake Bay and its tidal 
tributaries. / Exp. Mar. Biol. Ecol. 381 :S204-S215. 


28 










Chesapeake Bay Program. 1989. Chesapeake Bay Basin Monitoring Program Atlas. Volume II. 
Biological and Living Resource Monitoring Programs. CBP/TRS 35/89. Annapolis, Maryland. 

Cooper, S. R. and G. S. Brush. 1991. Long-term history of Chesapeake Bay anoxia. Science 
254:992- 996. 

Colman, S. M. and J. F. Bratton. 2003. Anthropogenically induced changes in sediment and 
biogenic silica fluxes in Chesapeake Bay. Geology 31 (1 ):71 -74. 

Cronin, T. M. and C. Vann. 2003. The sedimentary record of anthropogenic and climatic 
influence on the Patuxent estuary and Chesapeake Bay ecosystems. Estuaries 26 (2A). 

Karlsen, A. W., T. M. Cronin, S. E. Ishman, D. A. Willard, R. Kerhin, C. W. Holmes and M. 
Marot. 2000. Historical trends in Chesapeake Bay dissolved oxygen based on benthic 
foraminifera from sediment cores. Estuaries 23:488-508. 

Keller, A.A and L. Cavallaro. 2008. Assessing the US Clean Water Act 303d listing process for 
determining impairment of a waterbody. J. Env. Manage. 86:699-711. 

Llanso, R.J., D.M. Dauer and J.H. Volstad. 2009. Assessing ecological integrity for impaired 
waters decisions in Chesapeake Bay, USA. Marine Pollution Bulletin 59:48-53 

Scientific Technical Advisory Committee. 2006. The Cumulative Frequency Diagram Method 
for Determining Water Quality Attainment: Report of the Chesapeake Bay Program STAC Panel 
to Review of Chesapeake Bay Program Analytical Tools. STAC Publication 06-003. 74 pp. 

Scientific Technical Advisory Committee. 2009. Application or reference curves in dissolved 
oxygen criteria assessment. STAC Review and recommendations for the Chesapeake Bay 
Program. STAC Publ. 09-005. http://www.chesapeake.org/stac/Pubs/biorefcurvesreview.pdf 

U.S. Environmental Protection Agency. 2003. Ambient Water Quality Criteria for Dissolved 
Oxygen, Water Clarity and Chlorophyll a for the Chesapeake Bay and Its Tidal Tributaries 
(Regional Criteria Guidance). April 2003. EPA 903-R-03-002. Region III Chesapeake Bay 
Program Office, Annapolis, MD. 

U.S. Environmental Protection Agency. 2007. Ambient Water Quality Criteria for Dissolved 
Oxygen, Water Clarity and Chlorophyll a for the Chesapeake Bay and Its Tidal Tributaries - 
2007 Addendum. July 2007. EPA 903-R-07-003. Region III Chesapeake Bay Program Office, 
Annapolis, MD. 

U.S. Environmental Protection Agency. 2008. Ambient Water Quality Criteria for Dissolved 
Oxygen, Water Clarity and Chlorophyll a for the Chesapeake Bay and Its Tidal Tributaries-2008 
Technical Support for Criteria Assessment Protocols Addendum. September 2008. EPA 903-R- 
08-001. Region III Chesapeake Bay Program Office, Annapolis, MD. 


29 



Weisburg, S.B, J.A. Ranasinghe, D.M. Dauer, L.C. Schaffner, R.J. Diaz and J.13. Frithsen. 1997. 
An estuarine benthic index of biotic integrity (B-1B1) for Chesapeake Bay. 1997. Estuaries 
20:149-158. 

Zheng, Y..Weinman, B., Cronin, T., Fleisher, M.Q., Anderson, R.F., 2003. A rapid procedure for 
thorium, uranium, cadmium, and molybdenum in small sediment samples byinductively coupled 
plasma-mass spectrometry: application in Chesapeake Bay. 

Appl. Geochem. 18. 539-549. 

Zimmerman, A.R., Canuel, E.A., 2002. Sediment geochemical records of eutrophication 
in the mesohaline Chesapeake Bay. Limnol. Oceanogr. 47, 1084-1093. 


( 


30 


CHAPTER 4 


Revisions to the Chlorophyll a Criteria 
Assessment Methodology 

BACKGROUND 

In the 2003 Ambient Water Quality Criteria for Dissolved Oxygen , Water Clarity and 
Chlorophyll a for Chesapeake Bay and Its Tidal Tributaries, EPA published narrative 
chlorophyll a criteria that states chlorophyll a 

'‘...shall not exceed levels that result in ecologically undesirable consequences- 
such as reduced water clarity, low dissolved oxygen, food supply imbalances, 
proliferation of species deemed potentially harmful to aquatic life or humans or 
aesthetically objectionable conditions - or otherwise render tidal waters as 
unsuitable for designated uses balanced aquatic plant life populations and against 
the overgrowth of nuisance, potentially harmful species” (U.S. EPA 2003). 

From 2004 to 2006, Virginia and the District of Columbia adopted numerical chlorophyll a 
criteria for application in the tidal James River (Virginia) and across the District's jurisdictional 
tidal waters. In the 2007 publication Ambient Water Quality Criteria for Dissolved Oxygen, 
Water Clarity and Chlorophyll a for Chesapeake Bay and its Tidal Tributaries-2007 Addendum , 
EPA published chlorophyll a criteria assessment procedures (U.S. EPA 2007a, p. 62). With the 
establishment of numerical chlorophyll a concentration-based criteria promulgated by the states 
into their water quality standards regulations within Chesapeake Bay tidal waters, it was 
necessary to establish a reference curve for use in the published criteria attainment process (U.S. 
EPA 2003). 

A biologically-based reference curve with which to assess chlorophyll a criteria attainment in 
Chesapeake Bay is not yet available. A dataset has not been identified from which there is 
confidence that a biological reference curve can be derived (U.S. EPA 2007b). The EPA 
Chesapeake Bay Program Office and its partners, in consultation with regional experts in 
phytoplankton and chlorophyll a monitoring and research, have explored the published work of 
Buchanan et al. 2005 and Lacouture et al. 2006 conducted during development of the 
phytoplankton index of biotic integrity (P-IBI). 

In its current form, the published P-IBI work does not provide for a suitable representation of the 
integrated seasonal biological community conditions necessary to inform appropriate seasonal 
reference conditions for Chesapeake Bay chlorophyll a criteria attainment assessments. Benthic 
macroinvertebrates, for example, have life spans that integrate temporally variable environmental 
conditions over space, and the effects of multiple types of environmental stress and habitat 
alteration as used with the B-IBI for Chesapeake Bay (Llanso et al. 2009). However, standing 
crops of phytoplankton communities will respond to nutrient perturbations in 10-14 days 
(Heiskary and Walker 1995). Tracking the P-IBI results indicates any given segment can and 


31 


does move in and out of degradation within a single spring or summer season. Thus, the P-IB1 
does identify instances of high quality conditions, but currently does not provide the 
characteristics of a season-long “healthy” condition in terms of allowable exceedances that could 
be used to support derivation of a biologically-based reference for chlorophyll a criteria 
assessments. 

Further work is needed to specify a metric that can provide a priori identification of an 
unimpaired system on the relevant timescale, from which allowable exceedance of the 
chlorophyll a criteria can then be inferred. EPA, therefore, recommends a default 10% reference 
curve for assessing the chlorophyll a criteria (U.S. EPA 2007a, Figure 11-4, and Equation 1). 

REVIEW OF THE CURRENT CHLOROPHYLL A CRITERIA ATTAINMENT 
ASSESSMENT PROCEDURE: METHOD AND ASSUMPTIONS 

In Table IV-1, the current Chesapeake Bay chlorophyll a attainment assessment procedure is 
outlined for developing a seasonal mean for a Chesapeake Bay management segment to compare 
with published numerical criteria (e.g., Virginia tidal James River and the District of Columbia's 
tidal waters, U.S. EPA 2007a, Appendix C). 


Table IV-1. Outline of the previously published Chesapeake Bay chlorophyll a criteria 
attainment assessment methodology. __ 


Outline of chlorophyll a attainment assessement steps 

Comments 

Chlorophyll a data used for scenario assessments comprise all 
chlorophyll a values in the CIMS water quality database with layer 
flagged “S” for surface. 

For Virginia chlorophyll a assessments, 
use all publically available and 
appropriate surface data, i.e., CIMS data 
plus VIMS/HRSD DATAFLOW data. 
(U.S. EPA 2008 p.30). 

Data are organized into individual “cruise” files for interpolation. 


Individual cruise files are interpolated using the Chesapeake Bay 
Interpolator (version 4.61), with the “In-transform” and the “2-D 
Inverse-Distance Squared” options selected. 

The Interpolator automatically back- 
transforms chlorophyll a values in its 
output Files. (U.S. EPA 2008 p.30). 

Interpolated chlorophyll a surfaces are averaged for an entire season (on 
a cell-by-cell basis). 

The current methodology calculates an 
arithmetic mean on the back-transformed 
chlorophyll a values. 

Seasonal means are assessed (cell-by-cell) against the criterion for the 
relevant river segment-season. Assessment curves were compared 
against a default reference curve. Non-attainment is calculated by 
subtracting the area of the reference curve from the area under the 
chlorophyll a criteria assessment curve*. 

* If the assessment curve exceeds, at any 
point, the reference CFD, then the given 
segment is considered “impaired”. 


Source: U.S. EPA 2008 


To review the method details, U.S. EPA (2007a, p. 62) first states in the assessment procedure: 

“Assessments of seasonal mean chlorophyll a criteria should be based on 
seasonal averages of interpolated data sets. To calculate seasonal averages, 
each interpolated cruise within a season should be averaged on a point-by- 
point basis in matching interpolator grid cells. Spatial violation rates should be 
calculated for each seasonally aggregated interpolation in an assessment 
period. For example summer open water seasonal chlorophyll a criteria 


32 









assessment of a three-year assessment period, three seasonal average 
interpolations representing each season (Year I summer, Year 2 summer. 

Year 3 summer) should be used.” 

In the publication Ambient Water Quality Criteria for Dissolved Oxygen, Water Clarity and 
Chlorophyll a for Chesapeake Bay and its Tidal Tributaries-2008 Technical Support for Criteria 
Assessment Protocols Addendum , EPA provided further details documenting the chlorophyll a 
criteria assessment procedures (U.S. EPA 2008). Chapter 5 (U.S. EPA 2008, pp. 30-32) reviews 
the chlorophyll a criteria procedural steps to assess attainment while Appendix G (U.S. EPA 
2008) provides a highly detailed step-by-step process for completing the chlorophyll a criteria 
assessments. The application of data transformations to the chlorophyll a assessment data sets 
occurs during analyses in the process of calculating the seasonal mean (U.S. EPA 2008). 
Chapter 5, p. 30, Step 4 (U.S. EPA 2008) highlights the use of such a transformation on 
chlorophyll a data and states: 

“Data sets are imported into the Chesapeake Bay interpolator and transformed 
(natural log) prior to interpolation, as chlorophyll a measurements tend to follow a 
log-normal distribution. The program defaults for search area (25 km 2 ) and 
maximum sample size (4) are used, and the ‘2D Inverse Distance Squared’ 
algorithm is chosen. The Interpolator automatically back-transforms interpolated 
estimates before creating the output files.” 

Table IV-1 above shows the next step of computing a seasonal mean requires computation of an 
arithmetic mean over time at each point in the spatial interpolations represented by the 30-day 
means for the appropriate chlorophyll a criteria assessment season. 

First, while the mean is often used to report central tendency, for skewed data the arithmetic 
mean may not be in accord with the notion of ‘middle’. Skewed data make it unsuitable to 
estimate quantiles, proportions or means by normal distribution expectations (Gilbert 1987), i.e. 
an arithmetic mean. Tett and Wallis (1995) cite Barnes (1952) as indicating it is common for the 
variance of measurements on phytoplankton to be dependent on the mean. Sokal and Rohlf 
(1969) recommend logarithmic transformation of data exhibiting such characteristics. 

The previously published protocols for assessing Chesapeake Bay chlorophyll a criteria 
attainment were inconsistent in carrying out the seasonal mean computations since spatial 
interpolations are conducted on log transformed data while temporal averaging is conducted on 
untransformed data (U.S. EPA 2003, 2007a, 2008). Bland and Altman (1996) recommend that 
once data are transformed, carrying out all calculations on the transform scale and transform 
back once one has calculated the confidence intervals of the sample mean. 

Transformations on data provide the ability to approximate a statistical distribution based on the 
analyses to be performed using established inferential statistical procedures. When there is 
substantial skew in the data it is common to transform the data to a symmetric distribution. 
Analyses conducted with data approximating a normal distribution throughout the calculations 
then support the use of a wide array of well known statistical inference procedures based on well 
established statistics of the normal distribution. 


33 


Second, there is an underlying assumption to the calculations conducted as defined in the U.S. 
EPA 2007a and 2008 chlorophyll a criteria assessments that Chesapeake Bay chlorophyll data 
show log-normal tendencies. Based on this assumption, analyses depend on log-transforming of 
chlorophyll a data to provide a reasonable approximation of the normal distribution and support 
the use of normal distributional inference procedures. There is use of log-transformation 
chlorophyll a data in the Chesapeake Bay criteria literature cited in U.S. EPA 2007b, and there is 
a suggestion for positive skewness for chlorophyll a data shown with a hypothetical chlorophyll 
a data distribution (U.S. EPA 2007b). However, there is little background documenting the 
statistical distributional characteristics of Chesapeake Bay chlorophyll a data within the Ambient 
Water Quality Criteria for Dissolved Oxygen , Water Clarity and Chlorophyll a for Chesapeake 
Bay and its Tidal Tributaries publication series (U.S. EPA 2003, 2007a, 2007b, 2008). 

The following sections address: 1) peer-reviewed supporting literature regarding skewness and 
non-normality issues of chlorophyll a data; 2) log-normal transformation applications during 
analyses of Chesapeake Bay and other chlorophyll a data; and 3) recommended refinements to 
the published criteria assessment procedures. All these sections are directed towards providing 
consistency in computing the season mean of the 3-year assessments in logarithmic-space, 
thereby providing a sound estimate of central tendency for the final chlorophyll a assessment 
measures with the seasonal mean criteria. 

CHLOROPHYLL A: DATA SKEWNESS, LOG TRANFORMATION AND THE 

SEASONAL MEAN CALCULATION 

Log-normal Character of Chlorophyll a Data 

Support for the log-normal characteristics of chlorophyll a data have been published in the peer- 
reviewed scientific literature across a diversity of ecosystems. Harris (1986, Figure 9.7) 
illustrates seasonally dependent log-normal chlorophyll results for Hamilton Harbor (Lake 
Ontario). Vollenweider and Krekes (1980), as cited in Harris (1986), noted that algal biomass 
data from lakes was log-normally distributed. Recent work on Colorado lakes (n = 20) showed 
19 of 20 lakes chlorophyll measurements were well fit with log-normal transformations to 
approximate the normal distribution 4 . 

Within Chesapeake Bay, Jordan et al. (1991) describe correlations between watershed discharges 
and chlorophyll concentrations as complicated by non-normal distributions. Jordan et al. (1991) 
used the Box-Cox method (Sokal and Rohlf 1981) to identify the best power transformation for 
normalizing the data which was a log transformation. Harding (1994) showed that frequency 
distributions of chlorophyll and nutrient concentrations in Chesapeake Bay data were skewed; 
logarithmic transformations of the data produced normal distributions. 

4 http://\vAvw.chatfieldwatershedauthoritv.org / pdf/Characterizing%20Chlorophyll%20Distributions%2Qin%20Colora 

do.pdf 

Log-transforming Chesapeake Bay water quality indicator data (including chlorophyll) was 
integral to improvements of the Relative Status Indicator during its evolution (Olson 2009). 
Initially, Olson (2009) reports that positive skewed data led to unequal data distributions 


34 




affecting the outputs resulting in too many areas characterized as “good” when they were clearly 
unsatisfactory. Modifications applied to indicator calculations from 1998-2000, benchmark and 
status data sets (3-year windows) were log-transformed prior to analysis to address data 
skewness issues negatively impacting equality of data distribution characterizations. It was thus 
noted “that for water quality parameters the log and square root transformations are about equal 
in effecting a normal distribution of the data, and more effective than inverse transformations or 
using untransformed data” (Olson 2009). 

U.S. EPA (2007b) extended the published analyses of Harding (1994) and Harding and Perry 
(1997) modeling historical chlorophyll a data using a Generalized Linear Model (GLM) for logio 
(chlorophyll a). In deriving reference chlorophyll a criteria thresholds for Chesapeake Bay, 
thresholds were recommended as being derived by a model for the desired mean level of 
chlorophyll a in log space (U.S. EPA 2007b, page 17). Tables 111-2 and 111-3 in U.S. EPA 2007b, 
page 18) illustrate reference condition recommendations in log transform space mean 
chlorophyll and back transformed means. Recommendations for harmful algal bloom based 
chlorophyll a criteria in tidal fresh and oligohaline waters of Chesapeake Bay were further 
dependent upon log-transformed chlorophyll a analyses in their development (U.S. EPA 2007b). 

James River Focused Analyses of Log-transformed Chlorophyll a Data for Normality 

Tidal James River chlorophyll a data (1991-2000, n = 828) were log-transformed; natural 
logarithms were used. A Generalized Linear Modeling (GLM) approach was used to test 
chlorophyll a data for normality. Statistical Analysis Software (SAS) was used in the analysis. 
Seven Chesapeake Bay segments were included in the analysis: Mouth of Chesapeake Bay 
(CB8PH), Mouth to mid-Elizabeth River (ELIPH), Southern Branch Elizabeth River (SBEMH), 
Mouth of the James River (JMSPH), Lower James River (JMSMH), Middle James River 
(JMSOH) and Upper James River (JMSTF). Segments were grouped into one of four groups 
depending on similarity of their variances: 


then SegGrp = 1; 
then SegGrp = 2; 


"JMSPH" 

"JMSMH" "SBEMH" 
"JMSOH" "CB8PH" "ELIPH" 
'‘JMSTF" 


then SegGrp = 3; and 
then SegGrp = 4. 


The GLM model was ln(chlorophyll)= year, segment. (Equation 1) 


Data was analyzed by season. Spring was defined as March, April and May with summer defined 
as July, August and September. Normality diagnostics were reviewed for the raw residuals. 

For Spring and Summer seasons within the tidal James River, even without standardizing for 
heterogeneous variance, the ln(chla) residuals from the GLM model results show a fairly close 
approximation to a normal distribution. The normal probability plot shows very high 
concordance between the expected residuals and the observed residuals except for two outlier 
points in the extreme tails of the sample. These outliers probably reflect a failure of the simple 
model to capture some extreme event rather than a failure of log normality. The Shapiro-Wilk 
statistic of 0.994 (spring) and 0.988 (summer) shows that the residuals are very highly correlated 
with the expected residuals for approximating a normal distribution (see Appendix C). The 


35 


Shapiro-Wilks statistic ranges from 0 to 1 where 0 is farthest from normality and 1 is high 
fidelity with a normal distribution. The normality test p-value suggests a statistically significant 
departure from normality but this is not surprising with a sample size n = 828. The Shapiro- 
Wilks test is sensitive to small departures from normality with large sample sizes. The large 
sample size gives one the power to detect very small statistical differences from normality that, 
for analysis of the transformed data, are of low practical significance. Further details of the test 
output are provided in Appendix D. The SAS programs are included in Appendix E. 

CHLOROPHYLL A CRITERIA ASSESSMENT PROTOCOL REFINEMENTS 

USING LOG-TRANSFORMATIONS 

Statistical treatment of chlorophyll a data from a review of non-Chesapeake Bay and Chesapeake 
Bay specific peer reviewed scientific literature and U.S. EPA Chesapeake Bay criteria 
documentation: 1) supports a common recognition of skewness with chlorophyll a data sets; and 
2) shows a long history with the application of log-transformations for analyses. Bland and 
Altman (1996) recommend carrying out all calculations on the transform scale and transform 
back once one has calculated the confidence intervals of the sample mean. Log transformation of 
data during analyses to better reflect a normal distribution then better support the inference 
procedures based on normal distributions. The chlorophyll a criteria assessment protocol 
modifications described here (Table IV-2) constitute a more consistent and technically sound 
calculation than the currently published EPA methods (U.S. EPA 2003, 2007a, 2008). Analyses 
conducted with data approximating a normal distribution throughout the calculations supports 
the use of a wide array of statistical inference procedures based on normal distributions. Tidal 
James River chlorophyll a data was evaluated and showed fidelity to the normal distribution. 


( 


36 


Table IV-2. Previously published Chesapeake Bay chlorophyll a criteria assessment methods 
and recommended modifications. 


U.S. EPA 2008 Addendum 

U.S. EPA 2010 Addendum 

1. Chlorophyll a data used for scenario assessments 
comprise all chlorophyll a values in the C1MS 
water quality database with layer flagged “S” for 
surface. 

No modification recommended. 

2. Data are organized into individual ‘‘cruise” files for 
interpolation. 

No modification recommended. 

3. Individual cruise files are interpolated using the 
Chesapeake Bay Interpolator (version 4.61), with 
the "ln-transform” and the “2-D Inverse-Distance 
Squared” options selected. The Interpolator 
automatically back-transforms chlorophyll a 
values in its output files. 

No modification recommended. 

4. Interpolated chlorophyll a surfaces are averaged 
for an entire season (on a cell-by-cell basis). The 
current methodology calculates an arithmetic 
mean on the back-transformed chlorophyll a 
values 

4a. Interpolated chlorophyll a surfaces are In-transformed 
4b. Seasonal means are calculated on ln-transformed 
chlorophyll a values. 

5. Seasonal arithmetic means are assessed (cell-by¬ 
cell) against the criterion for the relevant river 
segment-season. 

5. Ln-transformed seasonal means are assessed (cell-by¬ 
cell) against the ln-transformed criterion for the 
relevant river segment-season. 


Source: U.S. EPA 2008. 


IMPLICATIONS OF THE REVISED ASSESSMENT PROTOCOL 

Conducting the spatial and temporal analyses in log-space produces geometric means. Geometric 
means will be less than the arithmetic means of the raw data, i.e. bias low for the estimator of the 
arithmetic mean, for all data sets with at least one pair of nonequal values (Bland and Altman 
1996). When all values in the data set are the same value and only then will the arithmetic mean 
equal the geometric mean. However, while geometric means may be less than arithmetic means, 
the values will always be above the minimum observed value and below the observed maximum 
value in both approaches. For log-normally distributed data such as the chlorophyll a data, the 
geometric mean is further a more efficient measure of central tendency, efficiently estimating the 
median which might be considered more typical of observations from the sampled population (E. 
Perry, 2010, Pers. Comm.). 

Given the very small number of data points in the tidal James River data analyses that influence 
the statistical measure of departure from normality, then this departure occurs in a small 
percentile of the distribution. Overall, the data align very well with the expected up through the 
10th percentile (see Appendix D). Because the CFD assessment method is defining the upper 
bound chlorophyll a criteria somewhere around the 10th percentile, it is fair to conclude that the 
log-normal is adequate for that purpose. While there may be another distribution that matches the 
data better than the normal distribution, one would, however, have to weigh the benefits of 
improved estimation against the costs of developing a suite of estimation procedures for this 
other distribution. One clear advantage of working with the log-normal is that the log 
transformation provides for a normal metric where one has many choices of well developed and 
well tested statistical methods (E. Perry 2010, Pers. Comm.). 


37 









The present Virginia water quality standards for tidal James River and the District of Columbia’s 
water quality standards for its tidal waters, stated as seasonal chlorophyll a means, reflect the 
importance of the assessment in measuring central tendency compared to an acceptable upper 
bound for acceptable water quality conditions. Chlorophyll a is a parameter whose measures 
repeatedly show skewed distributions appropriate to log transformation to approximate a normal 
distribution for making inference with well developed, well tested statistical methods. It is 
therefore appropriate to use a statistic that addresses the central tendency respecting the 
appropriate statistical properties of such data, i.e., the geometric mean. 

The EPA Chesapeake Bay Program Office and its partners tested the recommended revised 
assessment methodology for Chesapeake Bay data (e.g., tidal James River) and compared the 
results with the application of the promulgated Virginia water quality standards’ chlorophyll a 
criteria. Results showed almost universally greater levels of chlorophyll a attainment using the 
recommended revised methodology compared with the previously EPA published criteria 
assessment method (and adopted into Virginia’s water quality standards). Acknowledging these 
findings, the revisions to the published criteria assessment method are recommended for 
ensuring consistency within the assessment procedures with acknowledged the statistical 
properties of the chlorophyll a data. 


LITERATURE CITED 

Barnes, H. 1952. The use of transformations in marine biological statistics. J. du Conseil 18:61- 
71. 

Bland, J.M and D.G. Altman. 1996. Transformations, means and confidence intervals. British 
Medical Journal 312:1079. 

Buchanan, C., R. V. Lacouture, H. G. Marshall, M. Olson, J. Johnson. 2005. Phytoplankton 
reference communities for Chesapeake Bay and its tidal tributaries. Estuaries 28(1): 138-159. 

Colorado lakes study. 

http://www.chatfieldwatershedauthoritv.org/pdf/Characterizimz%20Chlorophyll%20Distribution 

s%20in%20Colorado.pdf 

Gilbert, R.O. 1987. Statistical methods for environmental pollution monitoring. Van Nostrand 
Reinhold, New York, NY.320 pp. 

Harding, L. Jr. 1994. Long term trends in the distribution of phytoplankton in Chesapeake Bay: 
roles of light, nutrients and streamflow. Mar. Ecol. Prog. Ser. 104:267-291. 

Harding, L.W., and E.S. Perry. 1997. Long-term increase of phytoplankton biomass in 
Chesapeake Bay, 1950-1994. Mar. Ecol. Prog. Series. 157:39-52. 




38 





Harris, G.P. 1986. Phytoplankton ecology: Structure, function and fluctuation. Chapman and 
Hall, New York, NY. 384 pp. 

Heiskary, Steven A and William W. Walkerjr. 1995. Establishing a chlorophyll agoal fora run- 
of-the-river reservoir. Lake and Re sere. Manage. 1 l(l):67-76. 

Jordan, T.E., D.L. Correll, J. Miklas, and D.E. Weller. 1991. Long-term trends in estuarine 
nutrients and chlorophyll, and short term effects of variation in watershed discharge. Mar. Ecol. 
Progr. Ser. 75:121-132. 

Lacouture, R.V., Johnson, J.M., Buchanan, C., and Marshall, H.G. 2006. Phytoplankton index of 
biotic integrity for Chesapeake Bay and its tidal tributaries. Estuaries Coasts 29: 598-616. 

Llanso, R.J., D.M. Dauer and J.H. Volstad. 2009. Assessing ecological integrity for impaired 
waters decisions in Chesapeake Bay, USA. Marine Pollution Bulletin 59:48-53 

Olson, M. 2009. Relative Status Indicator: Development and evolution of a relative measure of 
condition for assessing the status of water cpiality and biological parameters tracked in the U.S. 
EPA Chesapeake Bay Program long term monitoring programs. Final Report. September 2009. 
Chesapeake Bay Program Office, Annapolis, MD. 

Sokal, R.R. and F.J. Rohlf. 1981. Biometry, 2 nd ed. W.H. Freeman, San Francisco, CA. 

Tett, P. and A. Wallis. 1978. The general annual cycle of chlorophyll standing crop in Lock 
Creran. J. Ecol. 66:227-239. 

U.S. Environmental Protection Agency. 2003. Ambient Water Quality Criteria for Dissolved 
Oxygen, Water Clarity and Chlorophyll a for the Chesapeake Bay and Its Tidal Tributaries 
(Regional Criteria Guidance) April 2003. EPA 903-R-03-002. Region III Chesapeake Bay 
Program Office, Annapolis, MD. 

U.S. EPA 2007a. Ambient Water Quality Criteria for Dissolved Oxygen, Water Clarity and 

Chlorophyll a for the Chesapeake Bay and its Tidal Tributaries - 2007 Addendum. July 2007. 
EPA 903-R-07-003. Region III Chesapeake Bay Program Office, Annapolis, MD. 

U.S. EPA 2007b. Ambient Water Quality Criteria for Dissolved Oxygen, Water Clarity and 

Chlorophyll a for the Chesapeake Bay and its Tidal Tributaries - Chlorophyll Criteria 
Addendum. November 2007. EPA 903-R-07-005. Region III Chesapeake Bay Program Office, 
Annapolis, MD. 

U.S. EPA 2008. Ambient Water Quality Criteria for Dissolved Oxygen, Water Clarity and 
Chlorophyll a for the Chesapeake Bay and its Tidal Tributaries - 2008 Technical Support for 
Criteria Protocols Addendum. September 2008. EPA 903-R-08-001. Region III Chesapeake Bay 
Program Office, Annapolis, MD. 


39 


Vollenweider, R.A. and J. Krekes. 1980. The loading concept as a basis for controlling 
eutrophication: philosophy and preliminary results of the OECD programme on eutrophication. 
Prog. Wat. Tech not. 12:5-38. 


( 


40 


ACRONYMS 


2-D 

two-dimensional 

B-IBI 

benthic index of biotic integrity 

CBP 

Chesapeake Bay Program 

CIMS 

Chesapeake Information Management System 

CFD 

cumulative frequency distribution 

CHLA 

chlorophyll a 

DC 

deep channel 

DO 

dissolved oxygen 

DW 

deep water 

EPA 

U.S. Environmental Protection Agency 

GLM 

Generalized Linear Model 

HRSD 

Hampton Roads Sanitation District 

in 

meters 

mg/L 

milligrams per liter 

OW 

open water 

P-IBI 

phytoplankton index of biotic integrity 

S 

surface 

SAS 

Statistical Analysis Software 

SD 

Standard Deviation 

STAC 

Scientific and Technical Advisory Committee 

VIMS 

Virginia Institute of Marine Science 


Appendix A. 

B-IBI Sample Size and Standard Deviations on B-IBI 
Scoring when Screening Segments for Reference 
Community Characterization 

The EPA Chesapeake Bay Program Office in cooperation with its partners, examined the 
effects of relaxing the data screening criteria to accept segment-period combinations as 
“healthy” when defining reference communities with sample size > 8 (instead of the 
recommended n > 10) and/or standard deviation < 1.2 (instead of the recommended < 1.0). 
Data were 1996-2006 from the CIMS database. 

For the “fixed station” samples both “totalscore” and “grandscore” records were included. 
“Totalscore” records are replicate measurements of the same sampling event; the average of 
these is reported as the “grand score.” Benthic experts (Llanso, Versar, Inc.) recommend 
using the “grand score” in these analyses. Four scenarios were explored (Table A-l). The 
EPA accepted screening criteria is the default under Scenario A. Scenarios B, C and D 
relaxed the standard deviation, sample size and both sample size and standard deviation, 
respectively. 


Table Al. Healthy deep-water segments as characterized with four scenarios of screening 
criteria. The accepted screening criteria is Scenario A. __ 



Scenario A 

Scenario B 

Scenario C 

Scenario D 


(Default) 





B-IBI >3.0 

B-IBI >3.0 

B-IBI >3.0 

B-IBI >3.0 


n > 10 

n > 10 

n > 8 

n> 8 


S.D. < 1.0 

S.D. < 1.2 

S.D. < 1.0 

S.D. < 1.2 

Total number of 
“healthy” deep water 

10 

11 

13 

16 

segment-periods 






Relaxation of the criteria results in moderate increases (ranging from 1 to 6) in the number of 
segment-periods classified as “healthy.” Due to the increased risk of inaccurate 
classification, it is important to examine not just the number of additional segment-periods, 
but also the shape of these curves. If a curve is classified as “healthy” but its location in CFD 
space is consistent with DO violation CFDs of segment-periods classified as “degraded,” 
then it is reasonable to question whether an inaccurate classification has occurred. 

In the case of Scenario B (relaxing the standard deviation criterion from a maximum of 1.0 to 
a maximum of 1.2), a single curve (CB5MH 1999-2001) is added to the group of “healthy” 
segment-periods. In Figure A-l below, this curve is visible as a light blue line, while the 
population of 10 curves identified in Scenario A are presented by dark blue lines. Degraded 


42 








segment-periods are visible as red lines. The biologically-based reference curve generated 
from the 100 th percentile of “Scenario A” violations at each time step is visible as a yellow 
line. 



space 

Figure A-l. Scenario B - illustrates the impact of maintaining the sample size criterion of n 
>_10 while relaxing the standard deviation criterion from a maximum of 1.0 to a maximum of 
1.2 

The shape of the CB5MH 1999-2001 curve (light blue line in Figure A-l) raises the question 
of whether increasing the uncertainty of the screening criteria resulted in erroneous 
classification of this segment-period as healthy. In particular, the location of the top half of 
this curve in CFD space that is dominated by degraded curves decreases confidence in the 
accuracy of its classification. The addition of this curve, particularly in combination with the 
methodology of taking the 100 th percentile of each curve at each point in time, would 
increase the potential for the resulting biologically-based reference curve to allow rates of 
hypoxia that result in degradation of the benthic community. 

In the case of Scenario C, the standard deviation is kept consistent with the recommended 
screening criteria but the sample size criterion is relaxed from 10 to 8. This relaxation of the 
recommended criteria results in the classification of 3 additional segments as “healthy.” The 
CFD curves for these additional segments are shown as light blue curves in Figure A-2. 

While two of the additional curves (CB6PH 1998-2000 and CB6PH 2000-2002) fall within 
the cloud of violation rates deemed “acceptable,” one curve (CB3MH 1996-1998) once again 
extends into the cloud of data dominated by CFDs associated with degraded segment-periods 
(Figure A-2). As described earlier, this raises the concern that relaxation of the criteria has 
resulted in the inaccurate classification of a degraded segment-period as healthy. 


















The relaxation of both the sample size and the standard deviation criteria (Scenario D) 
increases the number of segment-periods classified as “healthy” from 10 to 16. However, 4 
of these additional CFD curves extend into “degraded” CFD space to a degree that calls into 
question the accuracy of their classification as healthy (Figure A-3). 



space 

Figure A-2. Scenario C - illustrates the impact from relaxing the sample size criterion from n 
> 10 to n > 8 while maintaining the standard deviation criterion of S.D. < 1.0. 

Relaxing the screening criteria for defining healthy segments based on the B-IB1 with respect 
to minimum sample size and maximum standard deviation increases the number of healthy 
segments that can be used to generate the biologically-based reference curve. However, the 
increased uncertainty of accurate classification resulting from relaxation of the criteria far 
outweighs the potential benefit of increased sample size. For the reference CIMS dataset, the 
EPA recommended methodology results in a total sample size of 24 segment-periods, of 
which 10 are classified as healthy and 14 are classified as degraded. Accounting for the trade 
offs with segment classification risks, this present method is supported as sufficient in 
generating a low risk sample size for elucidating the boundary between acceptable (i.e. those 
which allow a healthy benthic community to persist) and unacceptable violations of the deep¬ 
water DO criteria. 


44 















\ 



space 


Figure A-3. Scenario D - illustrates the impact from relaxing the sample size criterion from n > 
10 to n > 8 and the standard deviation criterion of SD < 1.0 to SD <1.2. 


) 


> 


45 

















Appendix B. 

Shape of the Biologically-based Reference Curve 

The shape of the biologically-based reference curve is an important factor in identifying 
acceptable violations of the Chesapeake Bay water quality criteria for dissolved oxygen. The 
shape of biologically derived reference curve has thus far reinforced the suitability of the 
hyperbolic 10% default reference curve when a biologically-based reference curve is 
unavailable. An alternative hypothesis, however, is that comparing the total area under a CFD 
assessment curve to the total area under the biologically-based reference curve is a better 
measure of the degree to which healthy biological communities can tolerate violations of the DO 
criteria than the existing “point” method. Arguments put forth to support this proposal include: 
(1) a segment-period may exceed the biologically-based reference curve in one area of CFD 
space while the overall area of its exceedance is within than that represented by the biologically- 
based reference curve; (2) there is high variability in the shape of CFD curves and the data do not 
allow identification of combinations of time and volume that lead to poor B-IBI scores in a 
segment; and (3) the proposed “area” method has lower error rates than the published “point” 
method, even with the modifications proposed by EPA to the latter method. 

With regard to arguments 1 and 2, application of the method modifications outlined in this 
addendum, Chesapeake Bay benthic communities are now being accurately classified as 
“healthy” or “degraded” when there is sufficient data to do so. As a result, the Chesapeake Bay 
data support a rather specific combination of time and volume that forms the boundary between 
healthy and degraded benthic communities in the deep-water designated use (Figure B-l). 



space 


Figure B-l. Dissolved oxygen violation curves associated with healthy (blue) and degraded (red) 
benthic communities in deep-water designated use habitats. The deep-water biologically-based 
reference curve (yellow) is also shown. 


46 

















) 


Using a dataset with all duplicate records appropriately removed and all appropriate screening 
criteria applied, the error rate for the “Point Method” is zero. In this case, all segment-periods 
classified as “healthy” using the recommended screening criteria (n >_10, SD < 1.0) pass the 
EPA recommended deep-water biologically-based reference curve, and all segment-periods 
classified as “degraded" fail the recommended biologically-based reference curve (Tables B-l 
and B-2). 


Table B-l. Segment classifications using the recommended screening criteria: deep-water 


designated use. 


Method 

Correct 

Incorrect 


Healthy Segments 
Passing 

Degraded 
Segments Failing 

Healthy Segments 
Failing 

Degraded Segments 
Passing 

Published “Point” 
Method 

100% 

100% 

0% 

0% 

Proposed “Area” 
Method 

100% 

100% 

0% 

0% 


Table B-2. Segment-period classifications under the recommended method: deep-water 


designated use. 


Method 

Correct 

Incorrect 


Healthy Segments 

Degraded Segments 

Healthy Segments 

Degraded 


Passing 

Failing 

Failing 

Segments Passing 

Published “Point” 

CB6PH 1996 1998 

PAXMH 1996 1998 



Method 

CB7PH 1996 1998 

POTMH 1996 1998 




CB6PH 1997 1999 

PAXMH 1997 1999 




CB7PH 1997 1999 

POTMH 1997 1999 




CB7PH 1998 2000 

POTMH 1998 2000 




CB6PH 1999 2001 

PAXMH 1999 2001 




CB7PH 1999 2001 

POTMH 1999 2001 




CB7PH 2000 2002 

PAXMH 2000 2002 




CB6PH 2004 2006 

RPPMH 2000 2002 




CB7PH 2004 2006 

PAXMH 2001 2003 
PAXMH 2002 2004 
PAXMH 2003 2005 
PAXMH 2004 2006 
RPPMH 2004 2006 



Proposed “Area” 

CB6PH 1996-1998 

POTMH 19992001 



Method 

CB6PH 1997-1999 

POTMH 19982000 




CB6PH 1999-2001 

RPPMH20022004 




CB6PH 2004-2006 

PAXMH 19992001 




CB7PH 1996-1998 

PAXMH20012003 




CB7PH 1997-1999 

PAXMH20042006 




CB7PH 1998-2000 

POTMH 19971999 




CB7PH 1999-2001 

PAXMH20032005 




CB7PH 2000-2002 

PAXMH20002002 




CB7PH 2004-2006 

POTMH 19961998 
RPPMH20002002 
PAXMH20022004 
PAXMH 19961998 
PAXMH 19971999 




> 


47 


















Both methods result in the same error rates when duplicate records are removed and EPA's 
criteria are applied to the classification of benthic communities. However, in contrast to 
Argument 2 as described above, it is EPA’s position that this dataset does provide convincing 
biological information with regard to the degree and distribution of deep-water DO criteria 
violations that can be tolerated by the benthic community. Furthermore, by using the worst 
violation rate allowed by any healthy community at each point in time, EPA has allowed for 
greater violation rates in regions of CFD-space where CFD curves from healthy and degraded 
communities overlap. It is reasonable to postulate, based on the distribution in CFD-space of 
curves associated with healthy and degraded benthic communities, that violations occurring in 
the CFD-space circled in black in Figure B-2 lead to degradation of the benthic community. 


o> 

E 



space 

Figure B-2. Violations occurring in the CFD-space circled in black are postulated to lead to 
degradation of the benthic community. 

It is suggested from the multiple lines of evidence that the shape of the biologically-based 
reference curve is an important factor in identifying acceptable violations of the DO criteria. The 
shape of this biological reference curve also provides further support for the suitability of the 
hyperbolic 10% reference curve, in that it illustrates the sensitivity of biological communities to 
chronic violations of DO criteria. 


48 




















Appendix C. 

Derivation of the Deep-Water Biologically-Based 

Reference Curve 


Step 1. We obtained a dataset of benthic scores for the Chesapeake Bay and tidal tributaries. 
Data used comprised benthic communities sampled between 1996 and 2006, from both the 
“fixed station” and “random strata” sampling programs. Only “grand score” values - which are 
an average of replicate samples - were included from the fixed station program. For the 
purposes of deriving a deep-water biological reference curve, we restricted the dataset to only 
those samples taken in segments that contain a deep-water designated use. 

Step 2. We removed from the dataset any samples obtained from the following segments: 
PATMH, SBEMH, and CB5MH. Benthic communities in PATMH and SBEMH are widely 
understood to be impacted by chemical contaminants (pers. comm, Roberto Llanso, Versar Inc.); 
a complication that confounds the relationship between hypoxia and benthic community health in 
these areas. 

In the case of CB5MH, areas greater than 12 meters in depth - which account for 35 percent of 
the bottom surface area of CB5MH - are excluded from the benthic sampling program because 
they are assumed to be azoic or nearly azoic. For their analyses of benthic health, Llanso et al. 
2009 assume that all areas greater than 12 m in depth are degraded, and perform a post-hoc 
correction to factor this assumption into their benthic assessment. For purposes of developing a 
biological reference curve, the exclusion from sampling of such a large portion of CB5MFI calls 
into question our ability to accurately characterize the health of its deep-water benthic 
communities. 

Step 3. We obtained water quality data from the Chesapeake Bay Program Water Quality 
database for the time period 1996-2006. Using the standardized method for locating pycnocline 
boundaries (see U.S. EPA 2008), we determined the depth of the upper and lower pycnocline 
boundaries for all sampling events in this time period. 

Step 4. From this dataset, we selected the sampling event that was closest in space (at a 
minimum, within the same segment) and time (at a minimum, within the same month) to each 
benthic sampling event. 

Step 5. We then classified each benthic sample as an “open-water,” “deep-water,” or “deep- 
channel” benthic sample based on its depth relative to the upper and lower pycnocline 
boundaries of the paired water quality sampling event. Benthic samples that were taken at 
depths between the upper and lower boundaries of the pycnocline were classified as “deep¬ 
water” samples. When no lower boundary was identified, benthic samples from depths below 
the upper boundary of the pycnocline were classified as “deep-water.” Benthic samples that 
could not be paired with a pycnocline boundary were discarded. 


49 


Step 6. For each 3-year time window from 1996-2006, we applied the following criteria to 
classify deep-water benthic communities as “healthy” for the purposes of generating a biological 
reference curve for the dissolved oxygen criteria assessment: at least 10 benthic 1BI scores; mean 
score > 3.0; and standard deviation of the mean < 1.0. Segment-periods (e.g. “CB6PH 1996- 
1998”) that met the above criteria were classified as “healthy.” 


Step 7. We obtained the “dissolved oxygen violation rates” for each healthy segment-period. 
These rates are an intermediate product of the dissolved oxygen criteria assessment procedure 
(see U.S. EPA 2007 and 2008). They represent the fraction of deep-water in a given segment 
that violates water quality criteria for dissolved oxygen in a given time period. Using these 
violation rates, we generated a CFD curve for each healthy segment-period. Most segment- 
periods contained 12 violation rates, but some contained only 11 rates. To account for segment- 
periods with different numbers of violation rates, all violation rates were interpolated to a 
common set of plotting positions (y values). To generate a biological reference curve that 
represented the “100 th percentile” of healthy violation rates, we then used the largest violation 
rate (across healthy segment-periods) for each “y” value of the violation CFD. The resulting set 
of violation rates represents the largest of all healthy violation rates for each plotting position. 
See chapter 3 for more details on the selection of the 100 th percentile curve. 

The following segment-periods comprised the set of “healthy” segment-periods: 

CB6PH 1996-1998 
CB7PH 1996-1998 
CB6PH 1997-1999 
CB7PH 1997-1999 
PAXMH 1997-1999 
CB7PH 1998-2000 
CB6PH 1999-2001 
CB7PH 1999-2001 
CB7PH 2000-2002 
CB7PH 2003-2005 
CB6PH 2004-2006 
CB7PH 2004-2006 


50 


) 


The resulting deep-water biologically-based reference curve for dissolved oxygen assessment is 
illustrated in Chapter 3, Figure 111-4 of this addendum and defined as: 


X 

Y 

(violation 

(plotting 

rate) 

position) 

0 

1 

0 

0.923077 

0 

0.846154 

0 

0.769231 

0.025641 

0.692308 

0.029132 

0.615385 

0.051185 

0.538462 

0.200524 

0.461538 

0.246642 

0.384615 

0.271513 

0.307692 

0.356639 

0.230769 

0.402786 

0.153846 

0.555376 

0.076923 

1 

0 


LITERATURE CITED 

Llanso, R.J., D.M. Dauer and J.H. Volstad. 2009. Assessing ecological integrity for impaired 
waters decisions in Chesapeake Bay, USA. Marine Pollution Bulletin 59:48-53 

U.S. Environmental Protection Agency. 2007. Ambient Water Quality Criteria for Dissolved 
Oxygen, Water Clarity and Chlorophyll a for the Chesapeake Bay and Its Tidal Tributaries - 
2007 Addendum. July 2007. EPA 903-R-07-003. Region III Chesapeake Bay Program Office, 
Annapolis, MD. 

U.S. Environmental Protection Agency. 2008. Ambient Water Quality Criteria for Dissolved 
Oxygen, Water Clarity and Chlorophyll a for the Chesapeake Bay and Its Tidal Tributaries 2008 
Technical Support for Criteria Assessment Protocols Addendum. September 2008. EPA 903-R- 
08-001. Region III Chesapeake Bay Program Office, Annapolis, MD. 


) 


51 



Appendix D. 

History of EPA Guidance Regarding the Deep-Channel 

Reference Curve 

In April 2003, the EPA published the guidance document. Ambient Water Quality Criteria for 
Dissolved Oxygen, Water Clarity and Chlorophyll a for the Chesapeake Bay and Its Tidal 
Tributaries (U.S. EPA 2003). In this publication, EPA documented the derivation of the 
dissolved oxygen criterion protective of the seasonal deep channel designated use. For seasonal 
deep-channel designated use, an instantaneous minimum criterion of 1 mg/L was determined to 
protect benthic organisms residing in the: 

“deep water-column and adjacent bottom surficial sediment habitats located 
principally in the river channel at the lower reaches of the major rivers and 
along the spine of the middle mainstem Chesapeake Bay at depths below 
which seasonal anoxic (< 0.2 mg/L dissolved oxygen) to severe hypoxic 
conditions (< 1 mg/L dissolved oxygen) routinely set in and persist for 
extended periods of time under current conditions” (p. 60 in U.S. EPA 2003). 

In support of the instantaneous minimum criterion of 1 mg/L, U.S. EPA (2003) summarized 
findings published in peer-reviewed literature sources indicating that several keystone benthic 
species “are resistant to dissolved oxygen concentrations as low as 0.6 mg/L,” and that 
“extensive mortality is likely only under persistent exposure to very low dissolved oxygen 
concentrations at high summer temperatures” (p. 61). 

U.S. EPA (2003) also reported that in the mesohaline Chesapeake Bay (the primary location of 
the seasonal deep-channel designated use), “dissolved oxygen concentrations of less than 1 mg/L 
lead to mortality for even tolerant species (p. 61) and that “when dissolved oxygen drops 
significantly below 1 mg/L for even short periods of time (on the order of hours) mortality 
increases, even for tolerant species” (p. 65). Furthermore, it was stated that “States and other 
users must recognize that the deep-channel dissolved oxygen criterion is stated as an 
instantaneous minimum, thus any exceedance is assumed to have direct consequences to the 
survival of the bottom-dwelling community” (p. 151). 

Regarding the definition of a water quality standard, it is explained in U.S. EPA 2003 and in 
Chapter 3 of the U.S. EPA’s Water Quality Standards Handbook, 2 nd Edition (U.S. EPA 1994) 
that water quality criteria definition and assessment comprises not just the magnitude of a water 
quality criterion (i.e. “the quantifiable condition,” in this case the concentration of dissolved 
oxygen), but also the duration and frequency of that condition. 

In this context, duration is addressed by restricting the applicability of the criterion to the 
summer period (June - September) when stratification and severe hypoxia occur in deep-channel 
regions of the Chesapeake Bay, and by defining the assessment period as “the most recent three 
consecutive years for which relevant monitoring data are available” (U.S. EPA 2003; p. 150-1). 


52 


The frequency component of the criterion “is directly addressed through comparison of the 
generated cumulative frequency distribution (CFD) with the applicable criterion reference curve” 
(U.S. EPA 2003;p. 151). 

In summary, statements were made in U.S. EPA 2003 suggesting that the benthic community can 
tolerate small violations of the deep-channel instantaneous minimum criterion, but statements 
were also made suggesting that any violation of this criterion has negative effects on the survival 
of deep-channel benthic species. However, as also described in U.S. EPA 2003, national 
guidelines define a water quality standard as comprising not only the magnitude of a given 
condition, but also the duration over which that condition is assessed and the frequency of 
violation allowed within the given assessment duration. For the case of the Chesapeake Bay, the 
frequency of allowable violation is defined by the location of a reference CFD, more commonly 
called a “reference curve" (both the rationale for use of a biological reference curve and the 
development of the 10 percent reference curve are also well documented in U.S. EPA 2003). 


LITERATURE CITED 

U.S. Environmental Protection Agency. 1994. Water Quality Standards Handbook, 2 nd Edition. 
August 1994. EPA 823-8-94-005a. Washington D.C. 

U.S. Environmental Protection Agency. 2003. Ambient Water Quality Criteria for Dissolved 
Oxygen, Water Clarity and Chlorophyll a for the Chesapeake Day and Its Tidal Tributaries 
(Regional Criteria Guidance). April 2003. EPA 903-R-03-002. Region III Chesapeake Bay 
Program Office, Annapolis, MD. 


53 



Appendix E. 

James River Chlorophyll a Data normality Analysis 
Checking Normality of Log-transformed Chlorophyll a 

Data 


Summary Notes regarding results of test log-normal assumption for James River chlorophyll. E. 
Perry 2/24/2010. 

SUMMER: 

Even without standardizing for heterogeneous variance, the ln(chl) residuals from the Year X 
Segment model seem to be fairly close to a normal distribution. The normality test show 
significant departure from normality 

• .It .If . I J. Ml _®tT_f \ 

• ^ •& ill 

Mtk\ Ifl^Qfifll^ + 

but this is not surprising with a sample size of 828. The large sample size gives you the power to 
detect very small differences from normality. The Shapiro-Wilk statistic of 0.988 shows that the 
residuals are very highly correlated with the expected residuals from a normal distribution. The 
normal probability plot shows very high concordance between the expected residuals and the 
observed residuals except for two outlier points in the extreme tails of the sample. These outliers 
probably reflect a failure of our simple model to capture some extreme event rather than a failure 
of log normality. 

Levene's test shows that the data do exhibit heterogeneous variances even in the log-metric. This 
heterogeniety seems to be associated with changing variance over segments. 

• .1 f . I 4. *4 Jf _®*Uf ^ 0— 

M.IH _• r ^f. « .. r .W 

•sA Wm «f i . U f ^ 


smi ■ eoir-iiiiii 

m . • .I.lllv 
m * + .I.Ul 


\ r s—ih 




Q 

. 1 • 


Q .f. ^ 

+ea O-. 


■ J* 

w i...*. 


.*.*1 ..III* 

A?' ? 


U_. *_ 


•; f A - *i 

..A 


O.fT 

. T oo 



1 

n 

i C*.X..W 

l.t.i.l W.l 




,i* f,.to 

..liiw 


54 



Standardizing the residuals by estimates of standard deviation by segment-group and year leads 
to improvement in both normality and homogeneous variance. However, both non-normality 
and heterogeneous variance remain statistically significant. 

Tests for Normality for standardized residuals 

A. • 4»a 444 44444 44444 

4*M^P « I.Ilf.I m . • l.Ittw 

■rfci m a + l.H w 

Levene’s test for standardized residuals 

^ ^1 • h9m ih «0* T 

Q . I . 

o.fA -*ai o» 4 ^ 


• St 

W X.iJl*.* 1. 

.... 1.11. 

At't 

.H *ll.Afl. 

fi. J. ♦ idtd-* 


• {f ” . •( —n 

. 1 *... *JI.llw 


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• 03 

•Si 

■4 

V 1 

* ...l.X.W 

¥ lw 

1....A 

•ota.ll* 

l.. *.f, aJ, 

dlA.Il.K 

I. HI. 


Again the heterogeniety seems to be associated with segments which suggests that the grouping 
algorithm could be improved. 


SPRING: 

Similar to summer results, without standardizing for heterogeneous variance, the In(chl) 
residuals from the Year X Segment model seem to be fairly close to a normal distribution. The 
normality test show significant departure from normality but the p-value is larger than for 
Summer. 

Tests for Normality for un-standardized residuals 

A • 44oaa*a 444 

GEa-J^l • l. lI ..*A 

mm'k ifi*a«jli* + 1.1*.!.. 

The Shapiro-Wilk statistic of 0.994 shows that the residuals are very highly correlated with the 
expected residuals from a normal distribution. The normal probability plot shows very high 
concordance between the expected residuals and the observed residuals and like the result for 
summer, the departure from normality appears as outlier points in the extreme tails of the 
sample. 

Levene’s test shows that the data do exhibit heterogeneous variances even in the log-metric. This 
heterogeniety seems to be associated with changing variance over both segments and years. 


mu -m mu 

*.. i.iu 
* * ♦ 


1.1*.* 


55 


aJfri★ 


* S l»lA_f k «L_ •★ 


in .^i* _• r ..f .U 


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■ J* 

A? I t 


Q .f. 



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A 

O-. . 

a^d o-.af^ 

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w 

* 


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A.. 


it,. 


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-A..,.!,.* 




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Bf 4 SI 




K.X^K. 

V..W..IA, 


K*1.*A,._ 

...i. lW t 


..* ..Hli 
..<* ..nii 


Standardizing the residuals by estimates of standard deviation by segment-group and year 
appears to resolve the heterogeneous variance issue but yields little improvement on normality. 

• ^ «l .if ■ f.B'fcB .if . sd af »^_f 


B*. 

b 4OM4& *81 44$ 45i44 - 

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l.A* 

I. A, 11 

A.. 

>★ AlA 

-id.A...d 

.11., wl.l* 

I. **.!*. 




56 



Appendix F. 

SAS Computer Code for James River Chlorophyll a 
Normality Tests, Spring and Summer Season 

★★★★★★★★★★★★★★★★★★★★★★★★★★★★★★★★★★ 

* PROGRAM: JAMES_RIVER.sas 

* This program will TEST CHLOROPHYLL DATA FOR NORMALITY 

* Base code from Elgin Perry 02/16/2010 

* additional code written by Jackie Johnson 02/17/2010 

/ 

libname ALGAE "G:\LR\OTHER_LR_DATA\Criteria_work\chlorophyll\2010"; 

*libname ALGAE "C:\Projects\CBP\CHLCRIT\LogNormal\"; 
options 1s = 7 2; 

*OPTIONS LS=120 PS=55 REPLACE NOCENTER; 

OPTIONS formchar = '|-|+|-+=|-/\<>*' ; 

* PROC IMPORT OUT= ALGAE.JAMES_SPRING_CHL 

DATATABLE= "JAMES_SPRING_CHL" 

DBMS=ACCESS2000 REPLACE; 

* 

DATABASE="G:\LR\OTHER_LR_DATA\Criteria_work\chlorophyll\2010\j ames_river.mdb" 
/ 

*RUN; 

* PROC CONTENTS DATA=ALGAE.JAMES SPRING CHL;RUN; 


data one; 

set ALGAE.JAMES_SPRING_CHL; 
logE_Chl = log(reported_value) ; 


label 

. logE Chl=" 

LOG_E UG/LITER" 

/ 

if 

cbseg 2003 

= 

"APPTF" 



or 

cbseg 2003 

= 

"CHKOH" 



or 

cbseg 2003 

= 

"EBEMH" 



or 

cbseg 2003 

= 

"LAFMH" 



or 

cbseg 2003 

= 

"WBEMH" 

then 

delete; 

if 

cbseg 2003 

= 

"JMSPH" 

then 

SegGrp = 1; 

if 

cbseg 2003 

= 

"JMSMH" 



or 

cbseg 2003 

= 

"SBEMH" 

then 

SegGrp = 2; 

if 

cbseg 2003 

= 

"JMSOH" 



or 

cbseg 2003 

- 

"CB8PH" 



or 

cbseg 2003 

= 

"ELIPH" 

then 

SegGrp = 3; 

if 

cbseg 2003 

= 

"JMSTF" 

then 

SegGrp = 4; 


sdate = DatePart(SAMPLE_DATE); 
year = year(SDATE); 

RUN; 

*Proc Contents; 

run ; 

title "Spring James River Data 1991-2000"; 

proc glm data=one; 

class year cbseg_2003; 

model logE_Chl=year cbseg_2003; 

output out= reschl r=rchl; 

run ; 

proc Univariate normal plot data=work.reschl; 
title2 "Normality test on raw residuals"; 


57 


var rchl; 

run; 

*( step to get rid of heterogeneous variances; 

Proc Sort data=reschl; 
by SegGrp year; 

run; 

Proc Means data=reschl noprint; 
by SegGrp year; 
var rchl; 

output out=sdchl StdDev = sdchl n=n; 

run; 

*(proc print data=sdchl; 

*( title "standard deviation results"; 

*( var SegGrp year sdchl n; 
data ResChl; 

merge ResChl sdchl; 
by SegGrp year; 

StdResChl = rchl/sdchl; 
run; 

proc Univariate normal plot data=work.reschl; 

title2 "Normality test on standardized residuals"; 
var StdResChl; 

run; 

* (proc contents data=work.reschl; 

*(run; 
data four; 

set work.reschl; 
aRChl= abs(RChl); 
aStdResChl= abs(StdResChl); 
run; 

proc glm data=work.four; 

title2 "Levene's test for both types of residuals"; 
class year cbseg_2003; 

model aRChl aStdResChl=year cbseg_2003; 

*(means cbseg_2003/snk; 

*(lsmeans cbseg_2003; 

run; 


★ ★★★★★★★★★★★★★★★★★★★★★★★★★★★★★★★★★ 

* PROGRAM: JAMES_RIVER.sas 

* This program will TEST CHLOROPHYLL DATA FOR NORMALITY 

* Base code from Elgin Perry 02/16/2010 

* additional code written by Jackie Johnson 02/17/2010 

* ★★★★★★★★★★★★★★★★★★★★★★★★★★★★★★★★★★ • 

t 

libname ALGAE "G:\LR\OTHER_LR_DATA\Criteria_work\chlorophyll\2010" 
*libname ALGAE "C:\Projects\CBP\CHLCRIT\LogNormal\"; 
options Is=72; 

♦OPTIONS LS=120 PS=55 REPLACE NOCENTER; 

OPTIONS formchar = '|-|+|- +=|-/\<>*'; 

♦PROC IMPORT 0UT= ALGAE.JAMES_SPRING_CHL 
DATATABLE= "JAMES_SPRING_CHL" 

DBMS=ACCESS20 0 0 REPLACE; 


DATABASE-"G:\LR\OTHER__LR_DATA\Criteria_work\chlorophyll\2010\j ames river.mdb" 
/ 

*RUN; 

* PROC CONTENTS DATA=ALGAE.JAMES_SUMMER_CHL; RUN; 
data one; 

set ALGAE.JAMES_SUMMER_CHL; 
logE_Chl=log(reported_value); 


label 

logE 

_Chl = " 

L0G_E UG/LITER" 

/ 

if 

cbseg 

2003 

= 

"APPTF" 



or 

cbseg 

2003 

= 

"CHKOH" 



or 

cbseg 

2003 

= 

"EBEMH" 



or 

cbseg 

'2003 

= 

"LAFMH" 



or 

cbseg 

'2003 

= 

"WBEMH" 

then 

delete; 

if 

cbseg 

2003 

= 

"JMSPH" 

then 

SegGrp = 1; 

if 

cbseg 

_2 0 03 

= 

"JMSMH" 



or 

cbseg 

[2003 

= 

"SBEMH" 

then 

SegGrp = 2; 

if 

cbseg 

_2 003 

= 

"JMSOH" 



or 

cbseg 

2003 

= 

"CB8PH" 



or 

cbseg 

_2 0 03 

= 

"ELIPH" 

then 

SegGrp = 3; 

if 

cbseg 

2003 

= 

"JMSTF" 

then 

SegGrp = 4 ; 


sdate = DatePart(SAMPLE_DATE); 
year = year(SDATE); 

RUN; 

*Proc Contents; 

run ; 

title "Summer James River Data 1991-2000"; 
proc glm data=one; 

class year cbseg_2003; 
model logE_Chl=year cbseg_2003; 
output out= reschl r=rchl; 
run ; 

proc Univariate normal plot data=work.reschl; 
title2 "Normality test on raw residuals"; 
var rchl; 

run; 

*( step to get rid of heterogeneous variances; 

Proc Sort data=reschl; 
by SegGrp year; 

run ; 

Proc Means data=reschl noprint; 
by SegGrp year; 
var rchl; 

output out=sdchl StdDev = sdchl n=n; 

run; 

*(proc print data=sdchl; 

*( title "standard deviation results"; 

*( var SegGrp year sdchl n; 
data ResChl; 

merge ResChl sdchl; 
by SegGrp year; 

StdResChl = rchl/sdchl; 
run; 

proc Univariate normal plot data=work.reschl; 

title2 "Normality test on standardized residuals"; 


59 


var StdResChl; 

run; 

* (proc contents data=work.reschl; 

*(run; 
data four; 

set work.reschl; 
aRChl= abs(RChl); 
aStdResChl= abs(StdResChl); 
run; 

proc glm data=work.four; 

title2 "Levene's test for both types of residuals"; 
class year cbseg_2003; 

model aRChl aStdResChl=year cbseg_2003; 

*(means cbseg_2003/snk; 

*(lsmeans cbseg_2003; 

run; 


60 



May 2010 

U.S. Environmental Protection Agency 
Region III 

Chesapeake Bay Program Office 
Annapolis, Maryland 

and 

Region III 

Water Protection Division 
Philadelphia, Pennsylvania 

in coordination with 

Office of Water 

Office of Science and Technology 
Washington, D.C. 

and 

The states of 

Delaware, Maryland, New York 
Pennsylvania, Virginia and 
West Virginia and the District of Columbia 


LC ACQUISITIONS 



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